def startup(self):
"""The starting point of the workflow. It runs everytime.
It 1) grab project name if given
2) grab and go to work directory
3) get and read template(s) options
"""
#1. Get projectName
self.projectName = None
if self.customTemplateFile:
self.projectName = os.path.splitext(
os.path.basename(self.customTemplateFile))[0]
print('Project name:', self.projectName)
#2. Go to the work directory
#2.1 Get workDir
if not self.workDir:
if autoPath and 'SCRATCHDIR' in os.environ and self.projectName:
self.workDir = os.path.join(os.getenv('SCRATCHDIR'),
self.projectName, 'PYSAR')
else:
self.workDir = os.getcwd()
self.workDir = os.path.abspath(self.workDir)
#2.2 Go to workDir
if not os.path.isdir(self.workDir):
os.makedirs(self.workDir)
print('create directory:', self.workDir)
os.chdir(self.workDir)
print("Go to work directory:", self.workDir)
#3. Read templates
#3.1 Get default template file
lfile = os.path.join(os.path.dirname(__file__),
'defaults/pysarApp_template.txt') #latest version
cfile = os.path.join(self.workDir,
'pysarApp_template.txt') #current version
if not os.path.isfile(cfile):
print('copy default template file {} to work directory'.format(
lfile))
shutil.copy2(lfile, self.workDir)
else:
#cfile is obsolete if any key is missing
ldict = readfile.read_template(lfile)
cdict = readfile.read_template(cfile)
if any([key not in cdict.keys() for key in ldict.keys()]):
print(
'obsolete default template detected, update to the latest version.'
)
shutil.copy2(lfile, self.workDir)
#keep the existing option value from obsolete template file
ut.update_template_file(cfile, cdict)
self.templateFile = cfile
# 3.2 read (custom) template files into dicts
self._read_template()
return
def check_obsolete_default_template(inps):
"""Update pysarApp_template.txt file if it's obsolete, a.k.a. lack new option names"""
template_file = os.path.join(inps.workDir, 'pysarApp_template.txt')
obsolete_template = False
current_dict = readfile.read_template(template_file)
latest_dict = readfile.read_template(inps.autoTemplateFile)
for key in latest_dict.keys():
if key not in current_dict.keys():
obsolete_template = True
if obsolete_template:
print('obsolete default template detected, update to the latest template options.')
shutil.copy2(inps.autoTemplateFile, inps.workDir)
template_file = ut.update_template_file(template_file, current_dict)
else:
print('latest template file detected:', template_file)
return template_file
def check_obsolete_default_template(template_file='./pysarApp_template.txt'):
"""Update pysarApp_template.txt file if it's obsolete, a.k.a. lack new option names"""
obsolete_template = False
current_dict = readfile.read_template(template_file)
latest_dict = readfile.read_template(TEMPLATE)
for key in latest_dict.keys():
if key not in current_dict.keys():
obsolete_template = True
if obsolete_template:
print(
'obsolete default template detected, update to the latest template options.'
)
with open(template_file, 'w') as f:
f.write(TEMPLATE)
template_file = ut.update_template_file(template_file, current_dict)
else:
print('default template file exists: ' + template_file)
return template_file
def _read_template(self):
# read custom template, to:
# 1) update default template
# 2) add metadata to ifgramStack file and HDF-EOS5 file
self.customTemplate = None
if self.customTemplateFile:
cfile = self.customTemplateFile
# Copy custom template file to INPUTS directory for backup
inputs_dir = os.path.join(self.workDir, 'INPUTS')
if not os.path.isdir(inputs_dir):
os.makedirs(inputs_dir)
print('create directory:', inputs_dir)
if ut.run_or_skip(out_file=os.path.join(inputs_dir,
os.path.basename(cfile)),
in_file=cfile,
check_readable=False) == 'run':
shutil.copy2(cfile, inputs_dir)
print('copy {} to INPUTS directory for backup.'.format(
os.path.basename(cfile)))
# Read custom template
print('read custom template file:', cfile)
cdict = readfile.read_template(cfile)
# correct some loose type errors
standardValues = {
'def': 'auto',
'default': 'auto',
'y': 'yes',
'on': 'yes',
'true': 'yes',
'n': 'no',
'off': 'no',
'false': 'no'
}
for key, value in cdict.items():
if value in standardValues.keys():
cdict[key] = standardValues[value]
for key in ['pysar.deramp', 'pysar.troposphericDelay.method']:
if key in cdict.keys():
cdict[key] = cdict[key].lower().replace('-', '_')
if 'processor' in cdict.keys():
cdict['pysar.load.processor'] = cdict['processor']
# these metadata are used in load_data.py only, not needed afterwards
# (in order to manually add extra offset when the lookup table is shifted)
# (seen in ROI_PAC product sometimes)
for key in ['SUBSET_XMIN', 'SUBSET_YMIN']:
if key in cdict.keys():
cdict.pop(key)
self.customTemplate = dict(cdict)
# Update default template file based on custom template
print('update default template based on input custom template')
self.templateFile = ut.update_template_file(
self.templateFile, self.customTemplate)
print('read default template file:', self.templateFile)
self.template = readfile.read_template(self.templateFile)
self.template = ut.check_template_auto_value(self.template)
# correct some loose setup conflicts
if self.template['pysar.geocode'] is False:
for key in ['pysar.save.hdfEos5', 'pysar.save.kmz']:
if self.template[key] is True:
self.template['pysar.geocode'] = True
print('Turn ON pysar.geocode in order to run {}.'.format(
key))
break
return
def read_template(inps):
print('\n********** Read Template File **********')
# default template
inps.templateFile = os.path.join(inps.workDir, 'pysarApp_template.txt')
if not os.path.isfile(inps.templateFile):
print('generate default template file: ' + inps.templateFile)
with open(inps.templateFile, 'w') as f:
f.write(TEMPLATE)
else:
inps.templateFile = check_obsolete_default_template(inps.templateFile)
# custom template
templateCustom = None
if inps.templateFileCustom:
# Copy custom template file to work directory
if ut.update_file(os.path.basename(inps.templateFileCustom),
inps.templateFileCustom,
check_readable=False):
shutil.copy2(inps.templateFileCustom, inps.workDir)
print('copy {} to work directory'.format(
os.path.basename(inps.templateFileCustom)))
# Read custom template
print('read custom template file: ' + inps.templateFileCustom)
templateCustom = readfile.read_template(inps.templateFileCustom)
# correct some loose type errors
for key in templateCustom.keys():
if templateCustom[key].lower() in ['default']:
templateCustom[key] = 'auto'
elif templateCustom[key].lower() in ['n', 'off', 'false']:
templateCustom[key] = 'no'
elif templateCustom[key].lower() in ['y', 'on', 'true']:
templateCustom[key] = 'yes'
for key in ['pysar.deramp', 'pysar.troposphericDelay.method']:
if key in templateCustom.keys():
templateCustom[key] = templateCustom[key].lower().replace(
'-', '_')
if 'processor' in templateCustom.keys():
templateCustom['pysar.load.processor'] = templateCustom[
'processor']
# Update default template with custom input template
print('update default template based on input custom template')
inps.templateFile = ut.update_template_file(inps.templateFile,
templateCustom)
if inps.generate_template:
raise SystemExit('Exit as planned after template file generation.')
print('read default template file: ' + inps.templateFile)
template = readfile.read_template(inps.templateFile)
template = ut.check_template_auto_value(template)
# Get existing files name: unavco_attributes.txt
try:
inps.unavcoMetadataFile = ut.get_file_list('unavco_attribute*txt',
abspath=True)[0]
except:
inps.unavcoMetadataFile = None
print('No UNAVCO attributes file found.')
return inps, template, templateCustom