def main():
par = rsf.Par(sys.argv)
ext = par.string('ext') # Filetype by extension
pflt = par.int('pflt', 0) # Print Files with Lines longer Than
if ext == None:
ext = 'c'
dirs_to_search = 'adm api framework pens plot su system user'.split()
if ext == 'py':
dirs_to_search.append('book')
if pflt > 0:
guilty_files = []
else:
# This list will have at position i the number of lines of that length
line_len_list = []
for d in dirs_to_search:
for root,dirs,files in os.walk(d):
# Avoid Subversion bookkeeping directories
if '.svn' not in root:
myfiles = glob.glob(os.path.join(root,'*.'+ext))
if ext == 'py':
local_sconstruct = os.path.join(root,'SConstruct')
if os.path.isfile(local_sconstruct):
myfiles.append(local_sconstruct)
if myfiles != []:
for file in myfiles:
f = open(file,'r')
for line in f:
lilen = len(line.rstrip())
if pflt > 0:
if lilen > pflt:
guilty_files.append(file)
break
else:
# Make sure line_len_list is long enough
l4 = len(line_len_list)
ldiff = lilen+1-l4
if ldiff > 0:
line_len_list.extend(ldiff*[0])
line_len_list[lilen] += 1
f.close()
if pflt > 0:
guilty_files.sort()
for file in guilty_files:
print(file)
else:
for i in range(len(line_len_list)):
print('%d\t%d' % (i, line_len_list[i]))
return unix_success
def run(main_func, cpar=[], nminarg=None, nmaxarg=None):
'For eliminating boilerplate code in main programs'
# main_func must take a single argument -- par
# cpar is compulsory parameter list
# nminarg: minimum number of command-line arguments to the program
# nmaxarg: max nr of CLI args to prog
if nminarg != None:
show_man_and_out(len(sys.argv) < nminarg+1)
if nmaxarg != None:
show_man_and_out(len(sys.argv) > nmaxarg+1)
par = rsf.Par(sys.argv) # Parse arguments into a parameter table
show_man_and_out(par.bool('help', False))
for p in cpar:
q = par.string(p)
show_man_and_out(q == None)
try:
status = main_func(par) # run the program
except m8rex.Error, e:
msg(e.msg, True)
status = unix_error
#!/usr/bin/env python
'C-Wave Backus Averaging (See Marion et al., 1994)'
import sys
import numpy as np
import rsf.api as rsf
import string
import math as mt
# Inputs
par = rsf.Par()
slowness_name = par.string('slowness') # Slowness from Logs
rhob_name = par.string('density') # Density from Logs
depth = rsf.Input() # Depth from Logs
slow = rsf.Input(slowness_name)
rhob = rsf.Input(rhob_name)
ratio = par.float("ratio") # Percent of dom wavelength
peak_f = par.float("peak_f") # Dom wavelength
depthsample = par.float("depthsample") # Depth Sampling
depth_bkn = rsf.Output() # Output depth sampling
vel_bkn = rsf.Output('vel_bk') # Backus Avg. velocity
slow_bkn = rsf.Output('slow_bk') # Backus Avg. slowness
rhob_bkn = rsf.Output('rhob_bk') # Averaged density
assert 'float' == depth.type
assert 'float' == slow.type
assert 'float' == rhob.type
def main(argv=sys.argv):
unix_success = 0
unix_error = 1
################ get user parameters
if len(argv) < 2: # print selfdoc and exit if no parameters
rsfprog.selfdoc()
return unix_error
par = rsf.Par(argv) # get parameters
levels = par.int('levels', 3)
# directory search depth
outfile_name = par.string('outfile')
# file name for detailed inventory table, default none
untested = par.bool('untested', False)
# list untested examples?
################ build list of search directories
books = []
for item in argv[1:]:
if '=' in item: continue # skip parameter items
if not os.path.exists(item): # does item exist?
sys.stderr.write("Directory '%s' does not exist.\n" % item)
continue
if not os.path.isdir(item): # is item a directory?
sys.stderr.write("File '%s' is not a directory.\n" % item)
continue
books.append(os.path.normpath(item))
if len(books) == 0: # nothing to search
sys.stderr.write("No directories to search.\n")
return unix_error
sys.stdout.write("Searching in: %s\n\n" % books)
################ open outut file
if outfile_name == None:
outfile = None
else:
outfile = open(outfile_name, 'w')
outfile.write('proj error ')
outfile.write('test error time ')
outfile.write('size type fig lock miss ext diff same dir\n')
################ search directory tree
sbool = {True: 'yes', False: 'no ', None: '- '}
serror = {0: 'ok ', 1: 'error'}
rsftest_errors = 0
rsftest_no = 0
figdir_no = 0
lockdir_no = 0
figs_missing = 0
figs_extra = 0
figs_diff = 0
rsftest_error_list = []
rsftest_no_list = []
figdir_no_list = []
lockdir_no_list = []
figs_missing_list = []
figs_extra_list = []
figs_diff_list = []
for bookdir in books:
for root, dirs, files in os.walk(bookdir):
if '.svn' in dirs: dirs.remove('.svn') # don't visit .svn dirs
reldir = root.replace(bookdir, "dummy", 1) # get relative dir name
level = len(reldir.split(os.sep)) - 1 # get dir level
if level < levels: continue # scan to depth 'levels' ...
if level == levels: del dirs[:] # ... but not beyond 'levels'
# skip dirs without SConstruct
if 'SConstruct' not in files: continue
rsfproj_vals = read_rsfproj(root, files) # read rsfproj file
rsftest_vals = read_rsftest(root, files) # read rsftest file
# count errors
if rsftest_vals['error'] == 1:
rsftest_errors = rsftest_errors + 1
rsftest_error_list.append(root)
if not rsftest_vals['exist']:
rsftest_no = rsftest_no + 1
rsftest_no_list.append(root)
if rsftest_vals['exist_fig'] == False:
figdir_no = figdir_no + 1
figdir_no_list.append(root)
if rsftest_vals['exist_lock'] == False:
lockdir_no = lockdir_no + 1
lockdir_no_list.append(root)
if rsftest_vals['miss'] > 0:
figs_missing = figs_missing + 1
figs_missing_list.append(root)
if rsftest_vals['extra'] > 0:
figs_extra = figs_extra + 1
figs_extra_list.append(root)
if rsftest_vals['diff'] > 0:
figs_diff = figs_diff + 1
figs_diff_list.append(root)
# write summary table
if outfile != None:
outfile.write('%s ' % sbool[rsfproj_vals['exist']])
outfile.write('%s ' % serror[rsfproj_vals['error']])
outfile.write('%s ' % sbool[rsftest_vals['exist']])
outfile.write('%s ' % serror[rsftest_vals['error']])
outfile.write('"%-24s" ' % rsftest_vals['time'])
outfile.write('%12s ' % int_string(rsfproj_vals['size']))
outfile.write('%s ' % rsfproj_vals['data'])
outfile.write('%s ' % sbool[rsftest_vals['exist_fig']])
outfile.write('%s ' % sbool[rsftest_vals['exist_lock']])
outfile.write('%3s ' % int_string(rsftest_vals['miss']))
outfile.write('%3s ' % int_string(rsftest_vals['extra']))
outfile.write('%3s ' % int_string(rsftest_vals['diff']))
outfile.write('%3s ' % int_string(rsftest_vals['same']))
outfile.write('%s\n' % root)
################ write summary
sys.stdout.write("Examples without an .rsftest file (%d):\n" % rsftest_no)
if untested:
rsftest_no_list.sort()
for item in rsftest_no_list:
sys.stdout.write("%s\n" % item)
sys.stdout.write("\n")
sys.stdout.write("Examples with .rsftest file errors (%d):\n" %
rsftest_errors)
rsftest_error_list.sort()
for item in rsftest_error_list:
sys.stdout.write("%s\n" % item)
sys.stdout.write("\n")
sys.stdout.write("Tested examples without a fig directory (%d):\n" %
figdir_no)
figdir_no_list.sort()
for item in figdir_no_list:
sys.stdout.write("%s\n" % item)
sys.stdout.write("\n")
sys.stdout.write("Tested examples without a lock directory (%d):\n" %
lockdir_no)
lockdir_no_list.sort()
for item in lockdir_no_list:
sys.stdout.write("%s\n" % item)
sys.stdout.write("\n")
sys.stdout.write("Tested examples with missing figs (%d):\n" %
figs_missing)
figs_missing_list.sort()
for item in figs_missing_list:
sys.stdout.write("%s\n" % item)
sys.stdout.write("\n")
sys.stdout.write("Tested examples with extra figs (%d):\n" % figs_extra)
figs_extra_list.sort()
for item in figs_extra_list:
sys.stdout.write("%s\n" % item)
sys.stdout.write("\n")
sys.stdout.write("Tested examples with non-matching figs (%d):\n" %
figs_diff)
figs_diff_list.sort()
for item in figs_diff_list:
sys.stdout.write("%s\n" % item)
sys.stdout.write("\n")
return unix_success
def main(argv=sys.argv):
unix_success = 0
unix_error = 1
################ get user parameters
if len(argv) < 2: # print selfdoc and exit if no parameters
rsfprog.selfdoc()
return unix_error
par = rsf.Par(argv) # get parameters
figdir = par.string('figdir') # fig directory, default = ./Fig
lockdir = par.string(
'lockdir') # lock directory, default = lock counterpart of figdir
list = par.string(
'list') # how much to list [none,diff,miss,all], default = all
show = par.string(
'show') # how much to show [none,diff,miss,all], default = none
rsftest = par.bool('rsftest', False) # write .rsftest file?
copy = par.bool('copy',
False) # copy different figs from figdir to lockdir?
# check list and show parameters
options = ['none', 'diff', 'miss', 'all']
if list is None: list = 'all'
if options.count(list) == 0:
print "Unknown list option: %s" % list
return unix_error
if show is None: show = 'none'
if options.count(show) == 0:
print "Unknown show option: %s" % show
return unix_error
################ get environment variables
# get $RSFFIGS variable
rsffigs = os.environ.get('RSFFIGS')
# use $RSFROOT/figs if $RSFFIGS not defined
if rsffigs == None:
rsffigs = os.path.join(RSFROOT, 'share', 'madagascar', 'figs')
# get $RSFALTFIGS variable
rsfaltfigs = os.environ.get('RSFALTFIGS')
# use rsffigs if $RSFALTFIGS not defined
if rsfaltfigs == None: rsfaltfigs = rsffigs
################ get directory paths
# get fig directory path
if figdir is None: figpath = os.path.abspath(os.path.join('.', 'Fig'))
else: figpath = os.path.abspath(figdir)
# get lock directory path
if lockdir is None:
# default to $RSFFIGS/book_tree
book_paths = book_path_split(figpath)
lockpath = os.path.expandvars(os.path.join(rsffigs, book_paths[1]))
# if $RSFSRC is defined and we are not in
# $RSFSRC/book/book_tree then
# default to $RSFALTFIGS/book_tree
if os.environ.get('RSFSRC') != None:
if book_paths[0] != os.path.expandvars(
os.path.join('$RSFSRC', 'book')):
lockpath = os.path.expandvars(
os.path.join(rsfaltfigs, book_paths[1]))
# use user-supplied lockdir
else:
lockpath = os.path.abspath(lockdir)
# check if fig & lock directories exist
exist_fig = os.path.exists(figpath)
exist_lock = os.path.exists(lockpath)
# print fig directory path
print ""
if exist_fig:
print "Fig directory:"
print figpath
else:
print "Fig directory does not exist:"
print figpath
# print lock directory path
print ""
if exist_lock:
print "Lock directory:"
print lockpath
else:
print "Lock directory does not exist:"
print lockpath
if (not exist_fig) or (not exist_lock):
if rsftest:
rsftest_write(exist_fig, exist_lock, None, None, None, None, None)
return unix_error
################ initialize variables
miss = 0
extra = 0
diff = 0
same = 0
files = {}
################ get file lists
# get lists of vpl files
figlist = vpl_list(os.listdir(figpath))
locklist = vpl_list(os.listdir(lockpath))
figlist.sort()
locklist.sort()
# merge vpl lists
for item in figlist:
files[item] = ' '
for item in locklist:
files[item] = ' '
filelist = files.keys()
filelist.sort()
################ find missing and different files
# find missing files
for item in filelist:
if figlist.count(item) == 0:
files[item] = ' -'
miss = miss + 1
for item in filelist:
if locklist.count(item) == 0:
files[item] = ' +'
extra = extra + 1
# find different files
print ""
binpath = os.path.join(RSFROOT, 'bin')
command = os.path.join(binpath, sfprefix + 'vplotdiff')
for item in filelist:
if files[item] == ' ':
figfile = os.path.join(figpath, item)
lockfile = os.path.join(lockpath, item)
check = os.system(' '.join(
[command, figfile, lockfile, '2>/dev/null']))
if check != 0:
if copy:
print "Copying %s from fig directory to lock directory." % item
shutil.copy(figfile, lockfile)
else:
files[item] = '%2d' % (check // 256)
diff = diff + 1
################ print file list and show selected figs
command = os.path.join(binpath, 'sfpen')
for item in filelist:
miss_check = (files[item] != ' ')
diff_check = ((files[item] != ' ') and (files[item] != ' -')
and (files[item] != ' +'))
list_check = (((list == 'all')) or ((list == 'miss') and miss_check)
or ((list == 'diff') and diff_check))
show_check = (((show == 'all')) or ((show == 'miss') and miss_check)
or ((show == 'diff') and diff_check))
if files[item] == ' -': figfile = ''
else: figfile = os.path.join(figpath, item)
if files[item] == ' +': lockfile = ''
else: lockfile = os.path.join(lockpath, item)
if list_check: print " %s %s" % (files[item], item)
if show_check: syswait(' '.join([command, figfile, lockfile]))
if files[item] == ' ': same = same + 1
print ""
print "Identical files: %3d" % same
print "Different files: %3d" % diff
print "Files missing from Fig: %3d" % miss
print "Extra files in Fig: %3d" % extra
print "Total vplot files: %3d" % len(filelist)
print ""
# write .rsftest file
if rsftest:
rsftest_write(exist_fig, exist_lock, miss, extra, diff, same, files)
return unix_success
def main(argv=sys.argv):
unix_success = 0
unix_error = 1
################ get user parameters
if len(argv) < 2: # print selfdoc and exit if no parameters
rsfprog.selfdoc()
return unix_error
par = rsf.Par(argv) # get parameters
levels = par.int('levels', 3)
# directory search depth
list = par.string('list')
# how much to list [all,filter,none], default = all
timer = par.string('timer')
# output execution time [log,file,none], default = none
rsfproj = par.string('rsfproj')
# rsfproj filter [yes,no,both], default = yes
size = par.int('size', 1024**2)
# max data size filter (MB)
size = size * 1024**2
uses = par.string('uses')
# uses filter, default = any
fetch_none = par.bool('nofetch', True)
# fetch-no-data filter
fetch_public = par.bool('public', False)
# fetch-public-data filter
fetch_private = par.bool('private', False)
# fetch-private-data filter
fetch_local = par.bool('local', False)
# fetch-local-data filter
command = par.string('command')
# command to execute in each directory, default = none
skipfile = par.string('skipfile')
# file with list of directories to skip
if list is None: list = 'all'
if list not in ['all', 'filter', 'none']:
sys.stderr.write('Unknown list option: %s\n' % list)
return unix_error
if timer is None: timer = 'none'
if timer not in ['log', 'file', 'none']:
sys.stderr.write('Unknown timer option: %s\n' % timer)
return unix_error
if rsfproj is None: rsfproj = 'yes'
if rsfproj not in ['yes', 'no', 'both']:
sys.stderr.write('Unknown rsfproj option: %s\n' % rsfproj)
return unix_error
if uses is None: uses = 'any'
if fetch_none is None: fetch_none = True
if fetch_public is None: fetch_public = False
if fetch_private is None: fetch_private = False
if fetch_local is None: fetch_local = False
################ build list of search directories
books = []
for item in argv[1:]:
if '=' in item: continue # skip parameter items
if not os.path.exists(item): # does item exist?
sys.stderr.write("Directory '%s' does not exist.\n" % item)
continue
if not os.path.isdir(item): # is item a directory?
sys.stderr.write("File '%s' is not a directory.\n" % item)
continue
books.append(os.path.normpath(item))
if len(books) == 0: # nothing to search
sys.stderr.write("No directories to search.\n")
return unix_error
sys.stdout.write("Searching in: %s\n\n" % books)
sys.stdout.flush()
################ read skipfile
g = {}
l = {}
if skipfile is not None: execfile(skipfile, g, l)
if 'skiplist' in l: skiplist = l['skiplist']
else: skiplist = []
################ get list of tools installed in $RSFROOT
tool_list = os.listdir(os.path.join(RSFROOT, "bin"))
################ search directory tree
if (list == 'all') or (list == 'filter'):
sys.stdout.write(
'command rsfproj data size directory\n')
sys.stdout.flush()
total_list = 0
total_size = 0
pass_list = 0
pass_size = 0
rsfproj_yes = 0
rsfproj_no = 0
rsfproj_error = 0
command_error = 0
data_unknown = 0
data_none = 0
data_public = 0
data_private = 0
data_local = 0
for bookdir in books:
for root, dirs, files in os.walk(bookdir):
if '.svn' in dirs: dirs.remove('.svn') # don't visit .svn dirs
reldir = root.replace(bookdir, "dummy", 1) # get relative dir name
level = len(reldir.split(os.sep)) - 1 # get dir level
if level < levels: continue # scan to depth 'levels' ...
if level == levels: del dirs[:] # ... but not beyond 'levels'
# skip dirs without SConstruct
if 'SConstruct' not in files: continue
# read rsfproj file
tuple = read_rsfproj(root, files)
(error, rsfproj_exist, uses_list, data_type, data_size) = tuple
if error == 1:
rsfproj_error = rsfproj_error + 1
string = " ********* .rsfproj error ********* %s\n"
sys.stdout.write(string % root)
sys.stdout.flush()
tools = 'yes'
for item in uses_list:
if (item not in tool_list): tools = 'no '
# calculate directory filter
options = (skiplist, rsfproj, uses, size, fetch_none, fetch_public,
fetch_private, fetch_local)
props = (root, rsfproj_exist, uses_list, data_type, data_size)
filter = calc_filter(options, props)
if filter == True:
pass_list = pass_list + 1
pass_size = pass_size + data_size
# print data for each directory
if (list == 'all') or ((list == 'filter') and (filter == True)):
total_list = total_list + 1
total_size = total_size + data_size
if filter: filter_command = 'yes'
else: filter_command = 'no '
if rsfproj_exist == 'yes': rsfproj_yes = rsfproj_yes + 1
if rsfproj_exist == 'no': rsfproj_no = rsfproj_no + 1
if data_type == 'unknown': data_unknown = data_unknown + 1
if data_type == 'none': data_none = data_none + 1
if data_type == 'public': data_public = data_public + 1
if data_type == 'private': data_private = data_private + 1
if data_type == 'local': data_local = data_local + 1
tuple = (filter_command, rsfproj_exist, data_type,
size_string(data_size), root)
sys.stdout.write('%s %-3s %10s %-7s %s\n' %
tuple)
sys.stdout.flush()
# execute command in directory
if (filter is True) and (command is not None):
string = " +++++++++ running command +++++++++ %s\n"
sys.stdout.write(string % root)
sys.stdout.flush()
tuple = command_wait(' '.join(['cd', root, ';', command]))
(exit, dt_user, dt_sys, dt_real) = tuple
if (timer == 'log'):
string = " user %6.2f sys %6.2f real %6.2f %s\n"
sys.stdout.write(string % (dt_user, dt_sys, dt_real, root))
if (timer == 'file'):
rsftimer_write(root, exit, dt_user, dt_sys, dt_real)
if (exit == 0):
string = " --------- command success --------- %s\n"
else:
string = " ********* command error ********* %s\n"
command_error = command_error + 1
sys.stdout.write(string % root)
sys.stdout.write("\n")
sys.stdout.flush()
sys.stdout.write("\n")
sys.stdout.write("Directories listed : %3d\n" % total_list)
sys.stdout.write("Total data size : %s\n" % size_string(total_size))
sys.stdout.write("\n")
sys.stdout.write("Directories with .rsfproj : %3d\n" % rsfproj_yes)
sys.stdout.write("Directories without .rsfproj : %3d\n" % rsfproj_no)
sys.stdout.write(".rsfproj errors : %3d\n" % rsfproj_error)
sys.stdout.write("\n")
sys.stdout.write("Directories for command : %3d\n" % pass_list)
sys.stdout.write("Total data size for command : %s\n" %
size_string(pass_size))
sys.stdout.write("Command errors : %3d\n" % command_error)
sys.stdout.write("\n")
sys.stdout.write("Directories using unknown external data : %3d\n" %
data_unknown)
sys.stdout.write("Directories using no external data : %3d\n" %
data_none)
sys.stdout.write("Directories using public external data : %3d\n" %
data_public)
sys.stdout.write("Directories using private external data : %3d\n" %
data_private)
sys.stdout.write("Directories using local data : %3d\n" %
data_local)
sys.stdout.write("\n")
return unix_success
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
import rsf.api as sf
import numpy as np
try: # Give precedence to local version
from hegilles import jitter
except: # Use distributed version
from rsf.user.hegilles import jitter
par = sf.Par()
input = sf.Input()
output = sf.Output()
n1 = input.int("n1")
n2 = input.int("n2")
ni = input.size(2)
assert ni == 1, "sfjitter needs 2D input"
perc = par.float("perc", .75) # percentage of traces to remove
assert (perc > 0 and perc < 1), "perc should be between 0 and 1"
jit = par.float("jit", 1 / (1 - perc)) # maximum gap factor
seed = par.int("seed", np.random.randn()) # seed for random number generator
def initialize_params(units, features):
np.random.seed(42)
params = {
"W1": 0.1 * randn(units, features),
"b1": np.zeros(shape=units),
"W2": 0.1 * randn(units),
"b2": np.zeros(shape=1)
}
return params
# Get input parameters and 'source' files. These are RSF objects that works as
# pointers to the actual data/file.
par_obj = rsf.Par()
x_train_obj = rsf.Input() # first input as default
y_train_obj = rsf.Input('ytrain')
x_val_obj = rsf.Input('xval')
y_val_obj = rsf.Input('yval')
# Assign output 'target' files.
loss_train_obj = rsf.Output() # first output as default
loss_val_obj = rsf.Output('lossval')
# Parse parameter values from input object.
num_epochs = par_obj.int('nepochs')
learning_rate = par_obj.float('lr')
hidden_units = par_obj.int('hidden') # number of hidden units
# Get size of the input arrays and load them. (Initialize + Read)
def show_slice(slice, pnt, nx, ny, title='Constant time slice'):
import matplotlib.pyplot as plt
import matplotlib.cm as cm
plt.imshow(slice,
interpolation='nearest',
cmap=cm.jet,
extent=(1, nx, 1, ny),
origin='lower')
plt.title(title)
plt.plot(pnt[:, 0], pnt[:, 1], 'k.')
plt.colorbar()
plt.show()
# get parameters from command line
command_line_par = rsf.Par()
#
# Survey parameters
nxline = command_line_par.int("nxline")
if nxline == None:
print "nxline is a required parameter in interpvel"
sys.exit(2)
ninline = command_line_par.int("ninline")
if ninline == None:
print "ninline is a required parameter in interpvel"
sys.exit(2)
fxline = command_line_par.int("fxline")
if fxline == None:
#print vs
# close files
for k in [vd, tvd]:
os.close(k)
for k in [vpath]:
os.remove(k)
vs.append(tvpath)
return
if __name__ == "__main__":
mgr = multiprocessing.Manager()
vs = mgr.list()
par = salah.Par()
n1 = par.int("n1") # size of the first axis
o1 = par.float("o1") # origin of the first axis
d1 = par.float("d1") # sampling in the first axis
#
if not (n1 or o1 or d1):
#sys.stderr.write(usage)
rsf.prog.selfdoc()
sys.exit(2)
if sys.stdout.isatty() or sys.stdin.isatty():
#sys.stderr.write(usage)
rsf.prog.selfdoc()
sys.exit(2)
inline = collections.OrderedDict()
loc = collections.OrderedDict()
i = None