def write_binary(filename,dic,data,overwrite=False,big=True):
"""
Write Bruker binary data to file
Parameters:
* filename Filename to write to.
* dic dictionary holding acqus_files and pprog_file parameters.
* data array of data
* overwrite True to overwrite files, False to warn.
* big Endiness to write binary data with,
bigendian=True, little=False
No return.
"""
# open the file for writing
f = fileiobase.open_towrite(filename,overwrite=overwrite)
# convert objec to an array if it is not already one...
if type(data) != np.ndarray:
data = np.array(data)
if np.iscomplexobj(data):
put_data(f,uncomplexify_data(data),big)
else:
put_data(f,data,big)
f.close()
return
def write_3D(filename, dic, data, overwrite=False):
"""
Write a sparky file from 3D data
"""
# open the file for writing
f = fileiobase.open_towrite(filename, overwrite)
# write the file header
put_fileheader(f, dic2fileheader(dic))
# write the axis headers
put_axisheader(f, dic2axisheader(dic["w1"]))
put_axisheader(f, dic2axisheader(dic["w2"]))
put_axisheader(f, dic2axisheader(dic["w3"]))
lentX = dic["w3"]["bsize"]
lentY = dic["w2"]["bsize"]
lentZ = dic["w1"]["bsize"]
t_tup = (lentZ, lentY, lentX)
ttX = np.ceil(data.shape[2] / float(lentX)) # total tiles in X dim
ttY = np.ceil(data.shape[1] / float(lentY)) # total tiles in Y dim
ttZ = np.ceil(data.shape[0] / float(lentZ)) # total tiles in Z dim
tt = ttX * ttY * ttZ
for i in xrange(int(tt)):
put_data(f, find_tilen_3d(data, i, (t_tup)))
f.close()
return
def write_binary_lowmem(filename,dic,data,overwrite=False,big=True):
"""
Write Bruker binary data to file trace by trace (using minimal memory).
Parameters:
* filename Filename to write to.
* dic dictionary holding acqus_files and pprog_file parameters.
* data array of data
* overwrite True to overwrite files, False to warn.
* big Endiness to write binary data with,
bigendian=True, little=False
No return.
"""
# open the file for writing
f = fileiobase.open_towrite(filename,overwrite=overwrite)
cplex = np.iscomplexobj(data)
# write out file trace by trace
for tup in np.ndindex(data.shape[:-1]):
trace = data[tup]
if cplex:
put_data(f,uncomplexify_data(trace),big)
else:
put_data(f,trace,big)
f.close()
return
def write_3D(filename,dic,data,overwrite=False):
"""
Write a sparky file from 3D data
"""
# open the file for writing
f = fileiobase.open_towrite(filename,overwrite)
# write the file header
put_fileheader(f,dic2fileheader(dic))
# write the axis headers
put_axisheader(f,dic2axisheader(dic["w1"]))
put_axisheader(f,dic2axisheader(dic["w2"]))
put_axisheader(f,dic2axisheader(dic["w3"]))
lentX = dic["w3"]["bsize"]
lentY = dic["w2"]["bsize"]
lentZ = dic["w1"]["bsize"]
t_tup = (lentZ,lentY,lentX)
ttX = np.ceil(data.shape[2] / float(lentX)) # total tiles in X dim
ttY = np.ceil(data.shape[1] / float(lentY)) # total tiles in Y dim
ttZ = np.ceil(data.shape[0] / float(lentZ)) # total tiles in Z dim
tt = ttX*ttY*ttZ
for i in xrange(int(tt)):
put_data( f,find_tilen_3d( data,i,(t_tup) ) )
f.close()
return
def write_jcamp(dic,filename,overwrite=False):
"""
Write a Bruker JCAMP-DX file from a dictionary
Written file will differ slightly from bruker's JCAMP-DX files in that all
multi-value parameters will be written on multiple lines. Bruker is
inconsistent on what is written to a single line and what is not.
In addition line breaks may be slightly different but will always be
within JCAMP-DX specification. Finally long floating point values
may loose precision when writing.
For example:
##$QS= (0..7)83 83 83 83 83 83 83 22
will be written as
##$QS= (0..7)
83 83 83 83 83 83 83 22
"""
# open the file for writing
f = fileiobase.open_towrite(filename,overwrite=overwrite)
# create a copy of the dictionary
d = dict(dic)
# remove the comments and core header key from dictionary
comments = d.pop("_comments")
corehdr = d.pop("_coreheader")
# write out the core headers
for line in corehdr:
f.write(line)
f.write("\n")
# write out the comments
for line in comments:
f.write(line)
f.write("\n")
keys = d.keys()
keys.sort()
# write out each key,value pair
for key in keys:
write_jcamp_pair(f,key,d[key])
# write ##END= and close the file
f.write("##END=")
f.close()
def write(filename, dic, data, dataset="spectrum", overwrite=False):
"""
Write dic,data pair to a HDF5 file
"""
# create the file
f = fileiobase.open_towrite(filename, overwrite=overwrite)
f.close()
f = h5py.File(filename, 'w')
# write the dictionary and data to the file
f.create_dataset(dataset, data=data)
put_dic(f, dic, dataset)
f.close()
return
def write(filename,dic,data,dataset="spectrum",overwrite=False):
"""
Write dic,data pair to a HDF5 file
"""
# create the file
f = fileiobase.open_towrite(filename,overwrite=overwrite)
f.close()
f = h5py.File(filename,'w')
# write the dictionary and data to the file
f.create_dataset(dataset,data=data)
put_dic(f,dic,dataset)
f.close()
return
def write(filename,comments,rec,overwrite=False):
"""
Write a nmrglue table to file (.tbl).
Parameters:
* filename Name of table file to write.
* comments List of comments (strings terminated with newline).
* rec Records array to write to file.
* overwrite Set True to overwrite file if it exists.
"""
# open the file for writing
f = fileiobase.open_towrite(filename,overwrite)
# write out the comment lines at the top of the file
for c in comments:
f.write(c)
# Determind the list of column names
names = rec.dtype.names
# Determind the list of column formats
sizes = [rec.dtype[n].itemsize for n in names]
kinds = [rec.dtype[n].kind for n in names]
formats = [k+str(s) for s,k in zip(sizes,kinds)]
# write out the NAMES and FORMATS lines
f.write("# NAMES "+" ".join(names)+"\n")
f.write("# FORMATS "+" ".join(formats)+"\n")
# maximum string length for each column
col_len = [max([len(str(i)) for i in rec[n]]) for n in names]
# write out each line of the table
for row in rec:
s = " ".join([str(v).ljust(l) for v,l in zip(row,col_len)])
f.write(s+"\n")
f.close()
def write_pprog(filename,dic,overwrite=False):
"""
Write a minimal Bruker pulse program
DO NOT TRY TO RUN THE RESULTING PULSE PROGRAM
This pulse program should return the same dictionary when read using
read_pprog, nothing else. The pulse program will be nonsense.
"""
# open the file for writing
f = fileiobase.open_towrite(filename,overwrite=overwrite)
# write a comment
f.write("; Minimal Bruker pulseprogram created by write_pprog\n")
# write our the variables
for k,v in dic["var"].iteritems():
f.write("\""+k+"="+v+"\"\n")
# write out each loop
for i,steps in enumerate(dic["loop"]):
# write our the increments
for v in dic["incr"][i]:
f.write("d01 id"+str(v)+"\n")
# write out the phases
for v,w in zip(dic["phase"][i],dic["ph_extra"][i]):
f.write("d01 ip"+str(v)+" "+str(w)+"\n")
f.write("lo to 0 times "+str(steps)+"\n")
# close the file
f.close()
return