/usr/bin/h5tospec is in python-sardana 1.6.1-1.
This file is owned by root:root, with mode 0o755.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 | #!/usr/bin/python
##############################################################################
##
## This file is part of Sardana
##
## http://www.tango-controls.org/static/sardana/latest/doc/html/index.html
##
## Copyright 2011 CELLS / ALBA Synchrotron, Bellaterra, Spain
##
## Sardana is free software: you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## Sardana is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU Lesser General Public License for more details.
##
## You should have received a copy of the GNU Lesser General Public License
## along with Sardana. If not, see <http://www.gnu.org/licenses/>.
##
##############################################################################
'''
Script for extracting "scans" from Sardana NeXus files into Sardana Spec Files.
Usage:
h5spec <nexusfilename> [> <your_spec_file_name>] [2><your error/log file]
Note: only scalar values are extracted, Images and 1D (MCA..) are ignored (notified to stderr)
'''
import nxs
import sys,os,re,time
def h52spectime(mydate):
'''
this function returns the time in format SPEC (from a hdf5 recorded by the sardanan recorder)
'''
#equivalent to ascii time
#return time.strftime("%a %b %d %H:%M:%S %Y",_d)
_a = time.asctime(time.strptime(mydate.split('.')[0],"%Y-%m-%dT%H:%M:%S"))
return _a
def _getMovables(mystr):
'''
this internal function gets the movables from the "scan/mesh" command.
Movables should go first in SPEC columns
'''
#gets the movables from the command line (starting not with a number)
_m = []
_a = mystr.split(' ')
_a.pop(0)
for i in _a:
if re.match('[^-_0-9\.\+\\n]',i):
_m.append(i)
return _m
def getMetadata(fd, entry):
'''
This gets the metatdata from the Sardana h5 file. Format is kind of free,
but nevertheless is very convenient the user/scientist makes sure all motors
(and motor positions) are there
'''
_mdata = {}
try:
fd.openpath("/%s/measurement/pre_scan_snapshot" % entry)
_mdata = fd.getentries()
for i in _mdata.keys():
fd.openpath("/%s/measurement/pre_scan_snapshot/%s" % (entry, i))
_mdata[i] = fd.getdata()
#print >> sys.stderr, entry
except:
print >> sys.stderr, 'Cannot open hdf5 path "%s/pre_scan_snapshot". Skipping.'%entry
return _mdata
def processEntry(fd, entry):
'''
process one entry from a hdf5 file
it creates a string with all the data and prints it to the stdout in the end.
It could be evenually easily modified to return the values and to be introduced
in a class (to get it out from this simple script)
'''
#_myMovables = [] # This gets the motors in order to write them in the first columns
mystring = "" # the string will construct the scan (and printed at the end)
try:
fd.openpath("/%s/entry_identifier" % entry)
mystring = "#S %s " % str(fd.getdata())
fd.openpath("/%s/title" % entry)
_mycmd = str(fd.getdata())
mystring += " %s \n" % _mycmd
_myMovables= _getMovables(_mycmd)
fd.openpath("/%s/start_time" % entry)
mystring += "#D %s \n" % h52spectime(fd.getdata())
# need to know here the timer for the counting time. In the mean time
# I use the last value of the cmd line (usually the ct time!!, not always ojo).
mystring += "#T %s (seconds)\n" % _mycmd.split(' ').pop()
#print mytime
except:
print >> sys.stderr, 'Error opening/processing hdf5 path "%s/...". Skipping.'% entry
mystring += "#P0 "
_metadata = getMetadata(fd, entry)
for i in _metadata.values():
mystring += ' ' + str(i)
mystring += '\n'
tmp = "/%s/measurement/point_nb" % entry
tmp2= "/%s/measurement/Pt_No" % entry
try:
fd.openpath(tmp)
except:
#print 'Cannot open hdf5 path "%s". Skipping.'%tmp
try:
fd.openpath(tmp2)
except:
#print 'Cannot open hdf5 path "%s". Skipping.'%tmp
return False
ptnb = fd.getdata()
fd.closedata()
headers = []
data = {}
for name,nxclass in fd.entries():
if name == 'point_nb' or name == "#Pt No": continue
if name == 'pre_scan_snapshot' : continue
dshape,dtype = fd.getinfo()
if tuple(dshape) != ptnb.shape:
print >> sys.stderr, "Skipping (no data or not a scalar ???) %s in %s" % (name, entry),
print >> sys.stderr, ptnb.shape
continue #not a scalar (incompatible shape)
#insert data and headers in the rigth order (movables first)
mydata = fd.getdata().flatten()
if name in _myMovables:
headers.insert(_myMovables.index(name), name)
else:
headers.append(name)
data[name] = mydata
mystring += "#N %d \n" % len(headers)
mystring += "#L "
for i in headers:
mystring += ' ' + i
mystring += "\n"
#print >>sys.stderr, headers
#print >>sys.stderr, _myMovables
#print >>sys.stderr, ptnb.size
#print >>sys.stderr, data
#print >>sys.stderr, ptnb
for i in range(ptnb.size):
# Movables (motors) come first. Then the other columns (exp channels)
for n in [channel for channel in _myMovables if channel in headers]:
mystring += ' ' + str(data[n][i])
for n in [channel for channel in headers if channel not in _myMovables]:
mystring += ' ' + str(data[n][i])
mystring += '\n'
try:
fd.openpath("/%s/end_time" % entry)
mystring += "#C Scan ended at %s \n" % h52spectime(fd.getdata())
except:
print >> sys.stderr, 'Cannot open hdf5 path "%s/end_time". Skipping.'% entry
print mystring
def measurement2spec(fd):
"""
Takes a file (hdf5) as an inputProcess a hdf5 file and outputs the result to the stdout.
One can redirect the output to create the file.
Information and error messages are output to stderr, in order not to pollute the file
"""
mystring = ""
mystring += "#F %s\n" % fd.filename
outFileAttrs = "#CCC original Nexus hdf5 file: %s\n" % fd.getattrs()
outCurrentDate = "#C conversion date: %s\n" % time.asctime()
entrynames = [name for name,c in fd.entries() if c=='NXentry']
mystring += "#E %s\n" % fd.getattrs()['epoch']
mystring += "#D %s\n" % time.asctime(time.localtime(fd.getattrs()['epoch']))
mystring += "#C User \n"
# Gets metadata headers (motor names usually) from the first entry (asuming all the same!)
_metadata = getMetadata(fd,entrynames[0])
mystring += "#O0"
for i in _metadata.keys():
mystring += ' ' + i
mystring += '\n' + outFileAttrs
mystring += outCurrentDate
print mystring
#Sort entry2 before entry10 (otherwhise, it was strictly alphabetic)
for entry in sorted(entrynames, key = len):
processEntry(fd, entry)
def main():
'''
process the entire file (todo: many things. Do only the selected entries, convert it to a class)
'''
if len(sys.argv) > 1:
fname = sys.argv[1]
else:
print "Usage:\npython h5tospec <nexusfilename> [> <your_spec_file_(or_to_console)> ] [2> log/error file]"
sys.exit(1)
fd = nxs.open(fname,'r')
measurement2spec(fd)
fd.close()
if __name__ == "__main__":
main()
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