def main(*args, **kwargs):
print 'Running "ms_merge" script'
# Find all multispec (.*vms.asc) files
specfiles = spec.find_multispec()
specfiles.sort()
# file reading and validating loop
exp_spectype = None
new_bundle = None
type_lkup = {'zv': spec.ZVSTSBundle, 'iv': spec.IVSTSBundle}
for file_path in specfiles:
try:
spectype = re.search(r'\.([zi]v)ms(?:\.asc)?$', file_path).group(1)
if exp_spectype is None:
exp_spectype = spectype
elif exp_spectype != spectype:
print 'Cannot mix spectroscopy types'
print 'ms_merge failed.'
return None
# END if
except AttributeError:
print '"{}" is not a multispec file'.format(file_path)
print 'ms_merge failed.'
return None
# END try
ms_data = type_lkup[spectype](file_path)
if new_bundle is None:
new_bundle = ms_data
elif list(new_bundle.X) != list(ms_data.X):
print 'Cannot concatenate multispecs with different domains'
print '{}:'.format(file_path)
print ' x_0 = {}'.format(ms_data.X[0])
print ' x_{} = {}'.format(ms_data.curve_len, ms_data.X[-1])
print 'Expected:'.format(file_path)
print ' x_0 = {}'.format(new_bundle.X[0])
print ' x_{} = {}'.format(new_bundle.curve_len, new_bundle.X[-1])
print 'ms_merge failed.'
return None
# END if
print u'\u2714 {}'.format(file_path)
new_bundle.concat(ms_data)
# END for
# Create file name
# ask for file name from user
new_name = raw_input('Please enter name for new multispec file:\n-->')
# remove any path syntax, force save in '.'
new_name = re.sub(r'^(.*?)([^/]+)$', r'\2', new_name)
# ensure the correct file extention, ".[zi]vms"
if not re.search(r'\.[zi]vms$', new_name):
new_name += '.' + exp_spectype + 'ms'
# END if
new_bundle.save_multispec(new_name)
print 'saved as "{}"'.format(new_name)
print 'ms_merge is finished.'
def main(*args, **kwargs):
print 'Running "ms_merge" script'
# Find all multispec (.*vms.asc) files
specfiles = spec.find_multispec()
specfiles.sort()
# file reading and validating loop
exp_spectype = None
new_bundle = None
type_lkup = {'zv': spec.ZVSTSBundle, 'iv': spec.IVSTSBundle}
for file_path in specfiles:
try:
spectype = re.search(r'\.([zi]v)ms(?:\.asc)?$', file_path).group(1)
if exp_spectype is None:
exp_spectype = spectype
elif exp_spectype != spectype:
print 'Cannot mix spectroscopy types'
print 'ms_merge failed.'
return None
# END if
except AttributeError:
print '"{}" is not a multispec file'.format(file_path)
print 'ms_merge failed.'
return None
# END try
ms_data = type_lkup[spectype](file_path)
if new_bundle is None:
new_bundle = ms_data
elif list(new_bundle.X) != list(ms_data.X):
print 'Cannot concatenate multispecs with different domains'
print '{}:'.format(file_path)
print ' x_0 = {}'.format(ms_data.X[0])
print ' x_{} = {}'.format(ms_data.curve_len, ms_data.X[-1])
print 'Expected:'.format(file_path)
print ' x_0 = {}'.format(new_bundle.X[0])
print ' x_{} = {}'.format(new_bundle.curve_len, new_bundle.X[-1])
print 'ms_merge failed.'
return None
# END if
print u'\u2714 {}'.format(file_path)
new_bundle.concat(ms_data)
# END for
# Create file name
# ask for file name from user
new_name = raw_input('Please enter name for new multispec file:\n-->')
# remove any path syntax, force save in '.'
new_name = re.sub(r'^(.*?)([^/]+)$', r'\2', new_name)
# ensure the correct file extention, ".[zi]vms"
if not re.search(r'\.[zi]vms$', new_name):
new_name += '.'+exp_spectype+'ms'
# END if
new_bundle.save_multispec(new_name)
print 'saved as "{}"'.format(new_name)
print 'ms_merge is finished.'
def main(path='./', flags=set()):
print 'Running "quick_plots_simple" script in {}'.format(path)
# Handle recursive search option
recursive = False
if 'r' in flags:
recursive = True
print '*Including all sub-folders'
# END if
# Handle the no-rewrite option
only_new = False
if 'n' in flags:
only_new = True
print '*Making new plots only'
# END if
# Find all multispec (.*vms.asc) files
specfiles = spec.find_multispec(path, recursive)
specfiles.sort()
# For no-rewrite option create a list of exclusions
if only_new:
skips = set()
files_stack = ['./'+f for f in os.listdir(path)]
while len(files_stack) > 0:
target = files_stack.pop()
name_match = re.search(
r'^.*?([^/]+?)-(?:zv|dzdv|iv|didv|ndidv)\.png$', target
)
if recursive and os.path.isdir(target):
for f in os.listdir(target): files_stack.append(target+'/'+f)
elif name_match and name_match.group(1) not in skips:
skips.add( name_match.group(1) )
# END if
# END while
# END if
# Plotting loop
for file_path in specfiles:
path_mat = re.search(r'^(.+?)([^/]+)$', file_path)
path = path_mat.group(1)
file_name = path_mat.group(2)
if (only_new
and re.sub(r'\.[zi]vms(?:\.asc)?', '', file_name) in skips):
continue
type_mat = re.search(r'\.([zi]v)ms(?:\.asc)?$', file_name)
spectype = type_mat.group(1)
if spectype == 'zv':
zv_subroutine(path, file_name)
elif spectype == 'iv':
iv_subroutine(path, file_name)
else:
print "don't know what to do with {}".format(file_name)
# END if
# END for
print 'quick_plots_simple is finished.'
def main(path='./', flags=set()):
print 'Running "quick_plots_simple" script in {}'.format(path)
# Handle recursive search option
recursive = False
if 'r' in flags:
recursive = True
print '*Including all sub-folders'
# END if
# Handle the no-rewrite option
only_new = False
if 'n' in flags:
only_new = True
print '*Making new plots only'
# END if
# Find all multispec (.*vms.asc) files
specfiles = spec.find_multispec(path, recursive)
specfiles.sort()
# For no-rewrite option create a list of exclusions
if only_new:
skips = set()
files_stack = ['./' + f for f in os.listdir(path)]
while len(files_stack) > 0:
target = files_stack.pop()
name_match = re.search(
r'^.*?([^/]+?)-(?:zv|dzdv|iv|didv|ndidv)\.png$', target)
if recursive and os.path.isdir(target):
for f in os.listdir(target):
files_stack.append(target + '/' + f)
elif name_match and name_match.group(1) not in skips:
skips.add(name_match.group(1))
# END if
# END while
# END if
# Plotting loop
for file_path in specfiles:
path_mat = re.search(r'^(.+?)([^/]+)$', file_path)
path = path_mat.group(1)
file_name = path_mat.group(2)
if (only_new
and re.sub(r'\.[zi]vms(?:\.asc)?', '', file_name) in skips):
continue
type_mat = re.search(r'\.([zi]v)ms(?:\.asc)?$', file_name)
spectype = type_mat.group(1)
if spectype == 'zv':
zv_subroutine(path, file_name)
elif spectype == 'iv':
iv_subroutine(path, file_name)
else:
print "don't know what to do with {}".format(file_name)
# END if
# END for
print 'quick_plots_simple is finished.'
def main(*args, **kwargs):
print 'Running "inspect" script'
# Find all multispec (.*vms.asc) files
specfiles = spec.find_multispec()
specfiles.sort()
# Curve plotting loop
type_lkup = {'zv': spec.ZVSTSBundle, 'iv': spec.IVSTSBundle}
for file_path in specfiles:
print 'Plotting all from "{}"'.format(file_path)
path_mat = re.search(r'^(.*?)\.([zi]v)ms(?:\.asc)?$', file_path)
new_foldername = path_mat.group(1)
spectype = path_mat.group(2)
all_curves = type_lkup[spectype](file_path)
# Make new folder for saving individual plots
if not os.path.exists(new_foldername):
os.makedirs(new_foldername)
X = all_curves.X
for i in range(all_curves.N):
save_path = new_foldername+'/curve_{0:03d}.png'.format(i)
if os.path.exists(save_path): continue
Y = all_curves.allY[i]
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(X, Y)
spec.pltformat_basic(ax)
ax.set_title( 'Curve i={}'.format(i) )
fig.savefig(save_path, dpi=100)
plt.close(fig)
# END for
# END for
print 'inspect is finished.'
def main_alt(path='./', flags=set()):
print 'Running "filename_fix" script'
# Simulate flag
simulate = False
if 's' in flags:
simulate = True
print '*Simulating file name changes'
# END if
# Find all multispec (.*vms.asc or .*vms) files
specfiles = spec.find_multispec(path)
specfiles.sort()
# file renaming loop
for file_path in allfiles:
fname = os.path.basename(file_path)
print '"{}"'.format(fname)
tags = re.search(r'''
^( \d{6} ) #0 date
( (?:-\d{4})? ) #1 time
( (?:-[^-]+)*? ) #2 pre-index
( -\d+ (?:_\d+ (?:_[fubd]+)?)? (?:-[A-Z]{1,2})? ) #3 index
( (?: -[^-]+ )* ) #4 post-index
( \.[zi]vms (?:\.asc)? )?$ #5 file-extention
''', fname, re.VERBOSE
).groups()
new_name = tags[0] + tags[1] + tags[2] + tags[4]
new_name += re.sub(r'(?<!^)-', '_', tags[3])
new_name += re.sub(r'\.asc', '', tags[5])
print ' -->"{}"'.format(new_name)
if not simulate and new_name != fname: os.rename(fname, new_name)
# END for
print 'filename_fix is finished.'
def main_alt(path='./', flags=set()):
print 'Running "filename_fix" script'
# Simulate flag
simulate = False
if 's' in flags:
simulate = True
print '*Simulating file name changes'
# END if
# Find all multispec (.*vms.asc or .*vms) files
specfiles = spec.find_multispec(path)
specfiles.sort()
# file renaming loop
for file_path in allfiles:
fname = os.path.basename(file_path)
print '"{}"'.format(fname)
tags = re.search(
r'''
^( \d{6} ) #0 date
( (?:-\d{4})? ) #1 time
( (?:-[^-]+)*? ) #2 pre-index
( -\d+ (?:_\d+ (?:_[fubd]+)?)? (?:-[A-Z]{1,2})? ) #3 index
( (?: -[^-]+ )* ) #4 post-index
( \.[zi]vms (?:\.asc)? )?$ #5 file-extention
''', fname, re.VERBOSE).groups()
new_name = tags[0] + tags[1] + tags[2] + tags[4]
new_name += re.sub(r'(?<!^)-', '_', tags[3])
new_name += re.sub(r'\.asc', '', tags[5])
print ' -->"{}"'.format(new_name)
if not simulate and new_name != fname: os.rename(fname, new_name)
# END for
print 'filename_fix is finished.'
def main(*args, **kwargs):
print 'Running "inspect" script'
# Find all multispec (.*vms.asc) files
specfiles = spec.find_multispec()
specfiles.sort()
# Curve plotting loop
type_lkup = {'zv': spec.ZVSTSBundle, 'iv': spec.IVSTSBundle}
for file_path in specfiles:
print 'Plotting all from "{}"'.format(file_path)
path_mat = re.search(r'^(.*?)\.([zi]v)ms(?:\.asc)?$', file_path)
new_foldername = path_mat.group(1)
spectype = path_mat.group(2)
all_curves = type_lkup[spectype](file_path)
# Make new folder for saving individual plots
if not os.path.exists(new_foldername):
os.makedirs(new_foldername)
X = all_curves.X
for i in range(all_curves.N):
save_path = new_foldername + '/curve_{0:03d}.png'.format(i)
if os.path.exists(save_path): continue
Y = all_curves.allY[i]
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(X, Y)
spec.pltformat_basic(ax)
ax.set_title('Curve i={}'.format(i))
fig.savefig(save_path, dpi=100)
plt.close(fig)
# END for
# END for
print 'inspect is finished.'
def main(path='./', flags=set()):
print sys.version
print 'Running "quick_plots" script in {}'.format(path)
# Handle recursive search option
recursive = False
if 'r' in flags:
recursive = True
print '*Including all sub-folders'
# END if
# Handle the no-rewrite option
only_new = False
if 'n' in flags:
only_new = True
print '*Making new plots only'
# END if
# Handle the multiprocessing options
top_gear = False
first_gear = False
if 'm' in flags:
first_gear = True
print '*Optioned to run everything under a single process'
elif 'M' in flags:
top_gear = True
print '*Optioned to run full number of processes'
# END if
# Find all multispec (.*vms.asc) files
specfiles = spec.find_multispec(path, recursive)
specfiles.sort()
# For no-rewrite option create a list of exclusions
if only_new:
skips = set()
files_stack = ['./'+f for f in os.listdir(path)]
while len(files_stack) > 0:
target = files_stack.pop()
name_match = re.search(
r'^.*?([^/]+?)-(?:zv|dzdv|iv|didv|ndidv)\.png$', target
)
if recursive and os.path.isdir(target):
for f in os.listdir(target): files_stack.append(target+'/'+f)
elif name_match and name_match.group(1) not in skips:
skips.add( name_match.group(1) )
# END if
# END while
# END if
# Setup the worker processes pool
N_procs = mproc.cpu_count()
if first_gear:
N_procs = 1
elif not top_gear:
# Default to using one less process than the total number of processors,
# for safety
N_procs -= 1
if N_procs == 0:
N_procs = 1
print (
'*Default safe running conditions will only use'
+ 'a single process on this system'
)
# END if
# END if
pool = mproc.Pool(processes=N_procs, maxtasksperchild=12)
# Plotting loop
for file_path in specfiles:
path_mat = re.search(r'^(.+?)([^/]+)$', file_path)
path = path_mat.group(1)
file_name = path_mat.group(2)
if (only_new
and re.sub(r'\.[zi]vms(?:\.asc)?', '', file_name) in skips):
continue
type_mat = re.search(r'\.([zi]v)ms(?:\.asc)?$', file_name)
spectype = type_mat.group(1)
if spectype == 'zv':
pool.apply_async(zv_subroutine, args=(path, file_name))
elif spectype == 'iv':
if os.path.exists(re.sub(r'\.ivms', '.gvms', file_path)):
pool.apply_async(giv_subroutine, args=(path, file_name))
else:
pool.apply_async(iv_subroutine, args=(path, file_name))
else:
print "don't know what to do with {}".format(file_name)
# END if
# END for
pool.close()
pool.join()
print 'quick_plots is finished.'
