def CODtoSHP(infile,outfile,stype):
#file names
#if len(sys.argv)==3:
codfile=infile
#else:
# codfile='I:/data/iris.cod'
# Modified by JPH on 8/3/2010 to allow for paths with '..'
#shpfile=outfile.split('.')[0]
shpfile=outfile;
##csvfile=shpfile+'_geo.csv'
##txtfile=shpfile+'_point.txt'
##polytxt=shpfile+'_poly.txt'
###################################Process COD###########################
#open files from parameters
inputCOD = open(codfile,'r')
centroidsDist=1
#get file header
#list of strings of fomatting
formatting=inputCOD.readline().split()
#inputCOD.readline()
#list of strings of column headings
names=[]
for i in range(1,int(formatting[0])+1):
names.append('att'+str(i))
header='Id,x,y'.split(',')+names
#+inputCOD.readline().strip('#n').split()
#parse cod
#list of strings lists of values
line=inputCOD.readline()
if line[0] == '#':
cod=[i.split() for i in inputCOD.readlines()]
else:
cod=[line.split()]+[i.split() for i in inputCOD.readlines()]
print len(cod),"records found\n"
inputCOD.close()
#get formatting
topology=formatting[1]
x=int(formatting[2])
y=int(formatting[3])
####################################Calculate centroidss####################
centroids=[]
#neurons listed from left to right, top to bottom
if topology=="rect":
for lcvY in range(y):
#loop over colomuns
for lcvX in range(x,0,-1):
centroids.append([float(lcvX*centroidsDist),float(lcvY*centroidsDist)])
elif topology=='hexa':
#caluclate the changes for centroids
deltaY=centroidsDist*sqrt(3.0/4)
deltaX=centroidsDist*float(1)
#set the orgin to start at 0,0 for the first point
hexX=0-deltaX
hexY=0
for lcvY in range(y):
for lcvX in range(x):
#increment x coordinate
hexX=hexX+deltaX
centroids.append([hexX,hexY])
#offset x coordinate for alternating rows
if (lcvY+1)%2:
hexX=0-(deltaX/2)
else:
hexX=0-deltaX
#increment y coordinate
hexY=hexY+deltaY
#####################################Calculate Polygons#######################
polygons=[]
if topology=="rect":
for i in centroids:
#center point
pX=i[0]
pY=i[1]
#derive extrema
minX=pX-(0.5*centroidsDist)
maxX=pX+(0.5*centroidsDist)
minY=pY-(0.5*centroidsDist)
maxY=pY+(0.5*centroidsDist)
#number of parts
NumParts=1
#total number of points
NumPoints=4
#bounding box
Box=[minX,minY,maxX,maxY]
#index to first point in part
Parts=0
#points for all parts
#starts from top most, left most, and goes clock-wise
Points=[Box,[[minX,maxY],[maxX,maxY],[maxX,minY],[minX,minY]]]
polygons.append(Points)
elif topology=='hexa':
for i in centroids:
#center point
pX=i[0]
pY=i[1]
#sides numberd in order of min length
side2=0.5*centroidsDist
side1=side2/sqrt(3)
side3=2*side1
#derive extreama
minX=pX-side2
maxX=pX+side2
minY=pY-side3
maxY=pY+side3
#bounding box
Box=[minX,minY,maxX,maxY]
#number of parts
NumParts=1
#number of points
NumPoints=6
#index to first point in part
Parts=0
#starts from top most, left most, and goes clock-wise
Points=[Box,[[pX,pY+side3],[pX+side2,pY+side1],[pX+side2,pY-side1],[pX,pY-side3],[pX-side2,pY-side1],[pX-side2,pY+side1]]]
polygons.append(Points)
######################################Construct Point Shapefile####################
shapes={}
shapes["point"]=1
shapes["polygon"]=5
shapeType=shapes[stype]
shp=open(shpfile+'.shp','wb') #main file
shx=open(shpfile+'.shx','wb') #index file
dbf=open(shpfile+'.dbf','wb') #dbf table
if shapeType==1:
#min expected at first point
Xmin=centroids[0][0]
Ymin=centroids[0][1]
#max expected at last point
Xmax=centroids[len(centroids)-1][0]
Ymax=centroids[len(centroids)-1][1]
elif shapeType==5:
#set default to first polygon
Xmin=polygons[0][0][0]
Ymin=polygons[0][0][1]
Xmax=polygons[0][0][2]
Ymax=polygons[0][0][3]
for i in polygons:
if i[0][0]<Xmin:
Xmin=i[0][0]
if i[0][1]<Ymin:
Ymin=i[0][1]
if i[0][2]>Xmax:
Xmax=i[0][2]
if i[0][3]>Ymax:
Ymax=i[0][3]
#version as set forth in 1998 whitepaper
version=1000
#Unused, with value 0.0, if not Measured or Z type
Zmin=0.0
Zmax=0.0
Mmin=0.0
Mmax=0.0
####################MAIN FILE and INDEX File#######################
if shapeType==1:
contentLength=10
elif shapeType==5:
#16+8*pnts
#contentLength=16+(8*len(polygons[0][1]))
if topology=='rect':
contentLength=64
elif topology=='hexa':
contentLength=80
########Main File Header##########
#BIG BYTE ORDER, integer
#byte 0, File Code
shp.write(struct.pack('>i', 9994))
#byte 4, Unused
shp.write(struct.pack('>i', 0))
#byte 8, Unused
shp.write(struct.pack('>i', 0))
#byte 12, Unused
shp.write(struct.pack('>i', 0))
#byte 16, Unused
shp.write(struct.pack('>i', 0))
#byte 20, Unused
shp.write(struct.pack('>i', 0))
#byte 24, File Length, total length of file in 16-bit words
#this must be determined after file creation.
shp.write(struct.pack('>i', 50+(contentLength*len(cod))))
#byte 28, Version, integer
shp.write(struct.pack('<i', version))
#byte 32, shape type
shp.write(struct.pack('<i',shapeType))
#byte 36, Bounding Box Xmin
shp.write(struct.pack('<d',Xmin))
#byte 44 Bounding Box Ymin
shp.write(struct.pack('<d',Ymin))
#byte 52 Bounding Box Xmax
shp.write(struct.pack('<d',Xmax))
#byte 60 Bounding Box Ymax
shp.write(struct.pack('<d',Ymax))
#byte 68* Bounding Box Zmin
shp.write(struct.pack('<d',Zmin))
#byte 76* Bounding Box Zmax
shp.write(struct.pack('<d',Zmax))
#byte 84* Bounding Box Mmin
shp.write(struct.pack('<d',Mmin))
#byte 92* Bounding Box Mmax
shp.write(struct.pack('<d',Mmax))
##############Index File Header###########
#BIG BYTE ORDER, integer
#byte 0, File Code
shx.write(struct.pack('>i', 9994))
#byte 4, Unused
shx.write(struct.pack('>i', 0))
#byte 8, Unused
shx.write(struct.pack('>i', 0))
#byte 12, Unused
shx.write(struct.pack('>i', 0))
#byte 16, Unused
shx.write(struct.pack('>i', 0))
#byte 20, Unused
shx.write(struct.pack('>i', 0))
#byte 24, File Length, total length of file in 16-bit words
shx.write(struct.pack('>i', 50+(4*len(cod))))
#byte 28, Version, integer
shx.write(struct.pack('<i', version))
#byte 32, shape type
shx.write(struct.pack('<i',shapeType))
#byte 36, Bounding Box Xmin
shx.write(struct.pack('<d',Xmin))
#byte 44 Bounding Box Ymin
shx.write(struct.pack('<d',Ymin))
#byte 52 Bounding Box Xmax
shx.write(struct.pack('<d',Xmax))
#byte 60 Bounding Box Ymax
shx.write(struct.pack('<d',Ymax))
#byte 68* Bounding Box Zmin
shx.write(struct.pack('<d',Zmin))
#byte 76* Bounding Box Zmax
shx.write(struct.pack('<d',Zmax))
#byte 84* Bounding Box Mmin
shx.write(struct.pack('<d',Mmin))
#byte 92* Bounding Box Mmax
shx.write(struct.pack('<d',Mmax))
if shapeType==1:
for id,i in enumerate(centroids):
#record header
#record numbers start at 1
shp.write(struct.pack('>i',id))
#content length
shp.write(struct.pack('>i',contentLength))
#record contents
#print float(i[0]),float(i[1])
shp.write(struct.pack('<i',shapeType))
shp.write(struct.pack('<d',float(i[0])))
shp.write(struct.pack('<d',float(i[1])))
#writing index records
#size=record header+content length
shx.write(struct.pack('>i',50+((contentLength+4)*id)))
shx.write(struct.pack('>i',contentLength))
elif shapeType==5:
for id,i in enumerate(polygons):
#record header
#record numbers start at 1
shp.write(struct.pack('>i',id))
#content length
shp.write(struct.pack('>i',contentLength))
#record contents
#print float(i[0]),float(i[1])
shp.write(struct.pack('<i',shapeType))
#bound box for polygon
for e in i[0]:
shp.write(struct.pack('<d',e))
#number of parts
shp.write(struct.pack('<i',1))
#number of points
shp.write(struct.pack('<i',len(i[1])+1))
#parts index
shp.write(struct.pack('<i',0))
#points
for p in i[1]:
#shape type for point
#shp.write(struct.pack('<i',1))
#x coordinate
shp.write(struct.pack('<d',float(p[0])))
#y coordinate
shp.write(struct.pack('<d',float(p[1])))
#print float(p[0]),float(p[1])
#x coordinate
shp.write(struct.pack('<d',float(i[1][0][0])))
#y coordinate
shp.write(struct.pack('<d',float(i[1][0][1])))
#writing index records
#size=record header+content length
shx.write(struct.pack('>i',50+((contentLength+4)*id)))
shx.write(struct.pack('>i',contentLength))
shp.close()
shx.close()
################DBF File###############
fieldnames = header[3:]
fieldwidth=max(max([map(len,i) for i in cod]))
deci=0
## for i in cod:
## for j in i:
## decimals=max(map(len,j.split('.')))
## if decimals > deci:
## deci=decimals
0
fieldspecs = [('N', fieldwidth, 6)]*(len(fieldnames)+1)
records = [([id+1]+map(round6,map(float,i))) for id,i in enumerate(cod)]
dbfwriter(dbf, ["NeuronID"]+fieldnames, fieldspecs, records)
dbf.close()
def ATRtoP(bmufile,outfile,stype):
#set shape file name
# Modified by JPH on 8/3/2010 to allow for paths with '..'
#shpfile=outfile.split('.')[0]
shpfile=outfile;
#open files
file1=open(bmufile,'r')
#extract formatting
formatting=file1.readline()
formatting=formatting.split()
topology=formatting[1]
#get column headers
names=['Qerror']
#split intput
lines=[convertNums(i.split()) for i in file1.readlines()]
####################################Calculate centroids and cod####################
centroids=[]
cod=[]
centroidsDist=1
#neurons listed from left to right, top to bottom
if topology=="rect":
for l in lines:
centroids.append([float(l[0]*centroidsDist),float(l[1]*centroidsDist)])
cod.append(l[2:])
elif topology=='hexa':
#caluclate the changes for centroids
deltaY=centroidsDist*math.sqrt(3.0/4)
deltaX=centroidsDist*float(1)
#set the orgin to start at 0,0 for the first point
for l in lines:
#if odd row
if (l[1]+1)%2:
hexX=l[0]
else:
hexX=l[0]+(0.5*centroidsDist)
hexY=(centroidsDist*0.5)*math.sqrt(3)*l[1]
n=random.random()
hexX=hexX+(math.cos(2*math.pi*n)*random.random()*(centroidsDist*0.3))
hexY=hexY+(math.sin(2*math.pi*n)*random.random()*(centroidsDist*0.3))
centroids.append([hexX,hexY])
cod.append(l[2:])
######################################Construct Point Shapefile####################
#In this section the shapefiles are written
#The 1998 white paper was use as the only reference for this section
#dictionary for shape types
shapes={}
shapes["point"]=1
shapes["polygon"]=5
shapeType=shapes[stype]
shp=open(shpfile+'.shp','wb') #main file
shx=open(shpfile+'.shx','wb') #index file
dbf=open(shpfile+'.dbf','wb') #dbf table
#if point file desired
if shapeType==1:
#min expected at first point
Xs=[centroids[i][0] for i in range(len(centroids))]
Ys=[centroids[i][1] for i in range(len(centroids))]
Xmin=min(Xs)
Ymin=min(Ys)
#max expected at last point
Xmax=max(Xs)
Ymax=max(Ys)
#version as set forth in 1998 whitepaper
version=1000
#Unused, with value 0.0, if not Measured or Z type
Zmin=0.0
Zmax=0.0
Mmin=0.0
Mmax=0.0
####################MAIN FILE and INDEX File#######################
#Main file and Index file creation begins here
#Integers are signed 32-bit integers (4 bytes)
#Doubles are signed 64-bit IEEE double-precision
#floating point numbers (8 bytes)
#lengths are measured in 16-bit words
#if point
if shapeType==1:
#shapetype+x+y=int+float+float=2+4+4
contentLength=10
elif shapeType==5:
if topology=="hexa":
contentLength=16+(4*7)
elif topology=="rect":
contentLength=16+(4*5)
########Main File Header##########
#This section corresponds directly to the whitepaper
#regarding main file creation
#BIG BYTE ORDER, integer
#byte 0, File Code
shp.write(struct.pack('>i', 9994))
#byte 4, Unused
shp.write(struct.pack('>i', 0))
#byte 8, Unused
shp.write(struct.pack('>i', 0))
#byte 12, Unused
shp.write(struct.pack('>i', 0))
#byte 16, Unused
shp.write(struct.pack('>i', 0))
#byte 20, Unused
shp.write(struct.pack('>i', 0))
#byte 24, File Length, total length of file in 16-bit words
shp.write(struct.pack('>i', 50+(contentLength*len(cod))))
#byte 28, Version, integer
shp.write(struct.pack('<i', version))
#byte 32, shape type
shp.write(struct.pack('<i',shapeType))
#byte 36, Bounding Box Xmin
shp.write(struct.pack('<d',Xmin))
#byte 44 Bounding Box Ymin
shp.write(struct.pack('<d',Ymin))
#byte 52 Bounding Box Xmax
shp.write(struct.pack('<d',Xmax))
#byte 60 Bounding Box Ymax
shp.write(struct.pack('<d',Ymax))
#byte 68* Bounding Box Zmin
shp.write(struct.pack('<d',Zmin))
#byte 76* Bounding Box Zmax
shp.write(struct.pack('<d',Zmax))
#byte 84* Bounding Box Mmin
shp.write(struct.pack('<d',Mmin))
#byte 92* Bounding Box Mmax
shp.write(struct.pack('<d',Mmax))
##############Index File Header###########
#This section corresponds directly to the whitepaper
#regarding index file creation
#BIG BYTE ORDER, integer
#byte 0, File Code
shx.write(struct.pack('>i', 9994))
#byte 4, Unused
shx.write(struct.pack('>i', 0))
#byte 8, Unused
shx.write(struct.pack('>i', 0))
#byte 12, Unused
shx.write(struct.pack('>i', 0))
#byte 16, Unused
shx.write(struct.pack('>i', 0))
#byte 20, Unused
shx.write(struct.pack('>i', 0))
#byte 24, File Length, total length of file in 16-bit words
shx.write(struct.pack('>i', 50+(4*len(cod))))
#byte 28, Version, integer
shx.write(struct.pack('<i', version))
#byte 32, shape type
shx.write(struct.pack('<i',shapeType))
#byte 36, Bounding Box Xmin
shx.write(struct.pack('<d',Xmin))
#byte 44 Bounding Box Ymin
shx.write(struct.pack('<d',Ymin))
#byte 52 Bounding Box Xmax
shx.write(struct.pack('<d',Xmax))
#byte 60 Bounding Box Ymax
shx.write(struct.pack('<d',Ymax))
#byte 68* Bounding Box Zmin
shx.write(struct.pack('<d',Zmin))
#byte 76* Bounding Box Zmax
shx.write(struct.pack('<d',Zmax))
#byte 84* Bounding Box Mmin
shx.write(struct.pack('<d',Mmin))
#byte 92* Bounding Box Mmax
shx.write(struct.pack('<d',Mmax))
#if point shape type
if shapeType==1:
#loop over all centroids and number them for ids
for id,i in enumerate(centroids):
#write record header
#record numbers start at 1
#however this seemingly works
shp.write(struct.pack('>i',id))
#content length
shp.write(struct.pack('>i',contentLength))
#write record contents
shp.write(struct.pack('<i',shapeType))
#write coordinates
shp.write(struct.pack('<d',float(i[0])))
shp.write(struct.pack('<d',float(i[1])))
#write index records
shx.write(struct.pack('>i',50+((contentLength+4)*id)))
shx.write(struct.pack('>i',contentLength))
#close files to empty buffer
shp.close()
shx.close()
################DBF File###############
#In this section the DBF for the shapefile is created
#This relies on a third party tool
#values are stored in their rounded-off amounts as numbers
#set column headers
fieldnames = names
#set column width
fieldwidth=[0]*len(cod[0])
for i in cod:
for id,j in enumerate(i):
if len(j)>fieldwidth[id]:
fieldwidth[id]=len(j)
#set field specs
# Changed by JPH on 8/3/2010 to allow 7 bytes in the field ID
#fieldspecs=[('N', 4, 6)]
fieldspecs=[('N', 7, 6)]
for w in fieldwidth:
fieldspecs.append(('N', w, 6))
#set records
records = [([id+1]+map(round6,map(float,i))) for id,i in enumerate(cod)]
#write dbf
dbfwriter(dbf, ["PointID"]+fieldnames, fieldspecs, records)
dbf.close()
shp.close()
shx.close()
################DBF File###############
fieldnames = header[3:]
fieldwidth=max(max([map(len,i) for i in cod]))
deci=0
## for i in cod:
## for j in i:
## decimals=max(map(len,j.split('.')))
## if decimals > deci:
## deci=decimals
0
fieldspecs = [('N', fieldwidth, 6)]*(len(fieldnames)+1)
records = [([id+1]+map(round6,map(float,i))) for id,i in enumerate(cod)]
dbfwriter(dbf, ["NeuronID"]+fieldnames, fieldspecs, records)
dbf.close()
######################################Ouput Options##########################
##outputPoly=open(polytxt,'w')
##outputPoly.write('Polygon\n')
##for id,l in enumerate(polygons):
## outputPoly.write(str(id)+' '+str(0)+'\n')
## for pid,p in enumerate(l[1]):
## outputPoly.write(str(pid)+' '+str(p[0])+' '+str(p[1])+'\n')
##outputPoly.write('END')
##outputPoly.close()
##
##outputTXT=open(txtfile,'w')
shp.write(struct.pack("<i", 0))
# points
shp.write(struct.pack("<d", Xmax))
shp.write(struct.pack("<d", Ymax))
shp.write(struct.pack("<d", Xmax))
shp.write(struct.pack("<d", Ymin))
shp.write(struct.pack("<d", Xmin))
shp.write(struct.pack("<d", Ymin))
shp.write(struct.pack("<d", Xmin))
shp.write(struct.pack("<d", Ymax))
shp.write(struct.pack("<d", Xmax))
shp.write(struct.pack("<d", Ymax))
# writing index records
# size=record header+content length
shx.write(struct.pack(">i", 50 + ((contentLength + 4) * id)))
shx.write(struct.pack(">i", contentLength))
shp.close()
shx.close()
dbfwriter(dbf, ["N"], [("N", 1, 0)], [[1]])
dbf.close()
shp.write(struct.pack('<i',len(centroids)))
#parts index
shp.write(struct.pack('<i',0))
#points
for p in centroids:
#shape type for point
#shp.write(struct.pack('<i',1))
#x coordinate
shp.write(struct.pack('<d',float(p[0])))
#y coordinate
shp.write(struct.pack('<d',float(p[1])))
#print float(p[0]),float(p[1])
#writing index records
#size=record header+content length
shx.write(struct.pack('>i',50))
shx.write(struct.pack('>i',contentLength))
shp.close()
shx.close()
################DBF File###############
fieldnames = ['Qerror']
fieldspecs = [('N', 16, 6)]
records = [[sum(cod)/len(cod)]]
dbfwriter(dbf, fieldnames, fieldspecs, records)
dbf.close()
ifile1=open(sys.argv[1],'rb')
ifile2=open(sys.argv[2],'rb')
ofile=open(sys.argv[3],'wb')
t1=dbftool.dbfreader(ifile1)
t2=dbftool.dbfreader(ifile2)
fn1=t1.next()
fn2=t2.next()
fn1.extend(fn2)
fs1=t1.next()
fs2=t2.next()
fs1.extend(fs2)
fnames=fn1
fspecs=fs1
recs1=[]
recs=[]
for i in t1:
recs1.append(i)
for i,j in enumerate(t2):
recs.append(recs1[i]+j)
dbftool.dbfwriter(ofile,fnames,fspecs,recs)
ofile.close()