def _aw_imager(self,
prepare_phase_output,
major_cycle,
sky_path,
skip=False):
"""
Create an image based on the calibrated, filtered and combined data.
"""
# Create parset for the awimage recipe
parset = self.parset.makeSubset("AWimager.")
# Get maxbaseline from 'full' parset
max_baseline = self.parset.getInt("Imaging.maxbaseline")
patch_dictionary = {"maxbaseline": str(max_baseline)}
try:
temp_parset_filename = patch_parset(parset, patch_dictionary)
aw_image_parset = get_parset(temp_parset_filename)
aw_image_parset_path = self._write_parset_to_file(
aw_image_parset, "awimager_cycle_{0}".format(major_cycle),
"Awimager recipe parset")
finally:
# remove tempfile
os.remove(temp_parset_filename)
# Create path to write the awimage files
intermediate_image_path = os.path.join(
self.scratch_directory, "awimage_cycle_{0}".format(major_cycle),
"image")
output_mapfile = self._write_datamap_to_file(
None, "awimager", "output map for awimager recipe")
mask_patch_size = self.parset.getInt("Imaging.mask_patch_size")
auto_imaging_specs = self.parset.getBool("Imaging.auto_imaging_specs")
fov = self.parset.getFloat("Imaging.fov")
specify_fov = self.parset.getBool("Imaging.specify_fov")
if skip:
pass
else:
# run the awimager recipe
self.run_task("imager_awimager",
prepare_phase_output,
parset=aw_image_parset_path,
mapfile=output_mapfile,
output_image=intermediate_image_path,
mask_patch_size=mask_patch_size,
sourcedb_path=sky_path,
working_directory=self.scratch_directory,
autogenerate_parameters=auto_imaging_specs,
specify_fov=specify_fov,
fov=fov)
return output_mapfile, max_baseline
def _aw_imager(self, prepare_phase_output, major_cycle, sky_path,
skip = False):
"""
Create an image based on the calibrated, filtered and combined data.
"""
# Create parset for the awimage recipe
parset = self.parset.makeSubset("AWimager.")
# Get maxbaseline from 'full' parset
max_baseline = self.parset.getInt("Imaging.maxbaseline")
patch_dictionary = {"maxbaseline": str(
max_baseline)}
try:
temp_parset_filename = patch_parset(parset, patch_dictionary)
aw_image_parset = get_parset(temp_parset_filename)
aw_image_parset_path = self._write_parset_to_file(aw_image_parset,
"awimager_cycle_{0}".format(major_cycle),
"Awimager recipe parset")
finally:
# remove tempfile
os.remove(temp_parset_filename)
# Create path to write the awimage files
intermediate_image_path = os.path.join(self.scratch_directory,
"awimage_cycle_{0}".format(major_cycle), "image")
output_mapfile = self._write_datamap_to_file(None, "awimager",
"output map for awimager recipe")
mask_patch_size = self.parset.getInt("Imaging.mask_patch_size")
autogenerate_parameters = self.parset.getBool(
"Imaging.auto_imaging_specs")
specify_fov = self.parset.getBool(
"Imaging.specify_fov")
if skip:
pass
else:
# run the awimager recipe
self.run_task("imager_awimager", prepare_phase_output,
parset = aw_image_parset_path,
mapfile = output_mapfile,
output_image = intermediate_image_path,
mask_patch_size = mask_patch_size,
sourcedb_path = sky_path,
working_directory = self.scratch_directory,
autogenerate_parameters = autogenerate_parameters,
specify_fov = specify_fov)
return output_mapfile, max_baseline
def run(self, executable, environment, parset, working_directory,
output_image, concatenated_measurement_set, sourcedb_path,
mask_patch_size, autogenerate_parameters, specify_fov, fov):
"""
:param executable: Path to awimager executable
:param environment: environment for catch_segfaults (executable runner)
:param parset: parameters for the awimager,
:param working_directory: directory the place temporary files
:param output_image: location and filesname to story the output images
the multiple images are appended with type extentions
:param concatenated_measurement_set: Input measurement set
:param sourcedb_path: Path the the sourcedb used to create the image
mask
:param mask_patch_size: Scaling of the patch around the source in the
mask
:param autogenerate_parameters: Turns on the autogeneration of:
cellsize, npix, wprojplanes, wmax, fov
:param fov: if autogenerate_parameters is false calculate
imageparameter (cellsize, npix, wprojplanes, wmax) relative to this
fov
:rtype: self.outputs["image"] The path to the output image
"""
self.logger.info("Start imager_awimager node run:")
log4_cplus_name = "imager_awimager"
self.environment.update(environment)
with log_time(self.logger):
# Read the parameters as specified in the parset
parset_object = get_parset(parset)
# *************************************************************
# 1. Calculate awimager parameters that depend on measurement set
# and the parset
cell_size, npix, w_max, w_proj_planes = \
self._get_imaging_parameters(
concatenated_measurement_set,
parset,
autogenerate_parameters,
specify_fov,
fov)
self.logger.info("Using autogenerated parameters; ")
self.logger.info(
"Calculated parameters: cell_size: {0}, npix: {1}".format(
cell_size, npix))
self.logger.info("w_max: {0}, w_proj_planes: {1} ".format(
w_max, w_proj_planes))
# ****************************************************************
# 2. Get the target image location from the mapfile for the parset.
# Create target dir if it not exists
image_path_head = os.path.dirname(output_image)
create_directory(image_path_head)
self.logger.debug("Created directory to place awimager output"
" files: {0}".format(image_path_head))
# ****************************************************************
# 3. Create the mask
mask_file_path = self._create_mask(npix, cell_size, output_image,
concatenated_measurement_set, executable,
working_directory, log4_cplus_name, sourcedb_path,
mask_patch_size, image_path_head)
# *****************************************************************
# 4. Update the parset with calculated parameters, and output image
patch_dictionary = {'uselogger': 'True', # enables log4cpluscd log
'ms': str(concatenated_measurement_set),
'cellsize': str(cell_size),
'npix': str(npix),
'wmax': str(w_max),
'wprojplanes': str(w_proj_planes),
'image': str(output_image),
'maxsupport': str(npix),
# 'mask':str(mask_file_path), #TODO REINTRODUCE
# MASK, excluded to speed up in this debug stage
}
# save the parset at the target dir for the image
calculated_parset_path = os.path.join(image_path_head,
"parset.par")
try:
temp_parset_filename = patch_parset(parset, patch_dictionary)
# Copy tmp file to the final location
shutil.copyfile(temp_parset_filename, calculated_parset_path)
self.logger.debug("Wrote parset for awimager run: {0}".format(
calculated_parset_path))
finally:
# remove temp file
os.remove(temp_parset_filename)
# *****************************************************************
# 5. Run the awimager with the updated parameterset
cmd = [executable, calculated_parset_path]
try:
with CatchLog4CPlus(working_directory,
self.logger.name + "." +
os.path.basename(log4_cplus_name),
os.path.basename(executable)
) as logger:
catch_segfaults(cmd, working_directory, self.environment,
logger)
# Thrown by catch_segfault
except CalledProcessError, exception:
self.logger.error(str(exception))
return 1
except Exception, exception:
self.logger.error(str(exception))
return 1
def _get_imaging_parameters(self, measurement_set, parset,
autogenerate_parameters, specify_fov, fov):
"""
(1) calculate and format some parameters that are determined runtime.
Based on values in the measurementset and input parameter (set):
a. <string> The cellsize
b. <int> The npixels in a each of the two dimension of the image
c. <string> The largest baseline in the ms smaller then the maxbaseline
d. <string> The number of projection planes
The calculation of these parameters is done in three steps:
1. Calculate intermediate results based on the ms.
2. The calculation of the actual target values using intermediate
result
"""
# *********************************************************************
# 1. Get partial solutions from the parameter set
# Get the parset and a number of raw parameters from this parset
parset_object = get_parset(parset)
baseline_limit = parset_object.getInt('maxbaseline')
# Get the longest baseline
max_baseline = pt.taql(
'CALC sqrt(max([select sumsqr(UVW[:2]) from ' + \
'{0} where sumsqr(UVW[:2]) <{1} giving as memory]))'.format(\
measurement_set, baseline_limit *
baseline_limit))[0] # ask ger van diepen for details if ness.
# Calculate the wave_length
table_ms = pt.table(measurement_set)
table_spectral_window = pt.table(
table_ms.getkeyword("SPECTRAL_WINDOW"))
freq = table_spectral_window.getcell("REF_FREQUENCY", 0)
table_spectral_window.close()
wave_length = pt.taql('CALC C()') / freq
wave_length = wave_length[0]
# Calculate the cell_size from the ms
arc_sec_in_degree = 3600
arc_sec_in_rad = (180.0 / math.pi) * arc_sec_in_degree
cell_size = (1.0 / 3) * (wave_length / float(max_baseline))\
* arc_sec_in_rad
# Calculate the number of pixels in x and y dim
# fov and diameter depending on the antenna name
fov_from_ms, station_diameter = self._get_fov_and_station_diameter(
measurement_set)
# use fov for to calculate a semi 'user' specified npix and cellsize
# The npix thus depends on the ms cellsize and fov
# Do not use use supplied Fov if autogenerating
if not autogenerate_parameters and specify_fov:
if fov == 0.0:
raise PipelineException("fov set to 0.0: invalid value.")
# else use full resolution (calculate the fov)
else:
self.logger.info("Using fov calculated on measurement data: " + str(fov_from_ms))
fov = fov_from_ms
# ********************************************************************
# 2. Calculate the ms based output variables
# 'optimal' npix based on measurement set calculations or user specified
npix = (arc_sec_in_degree * fov) / cell_size
# Get the closest power of two larger then the calculated pixel size
npix = self._nearest_ceiled_power2(npix)
# Get the max w with baseline < 10000
w_max = pt.taql('CALC max([select UVW[2] from ' + \
'{0} where sumsqr(UVW[:2]) <{1} giving as memory])'.format(
measurement_set, baseline_limit * baseline_limit))[0]
# Calculate number of projection planes
w_proj_planes = min(257, math.floor((max_baseline * wave_length) /
(station_diameter ** 2)))
w_proj_planes = int(round(w_proj_planes))
# MAximum number of proj planes set to 1024: George Heald, Ger van
# Diepen if this exception occurs
maxsupport = max(1024, npix)
if w_proj_planes > maxsupport:
raise Exception("The number of projections planes for the current"
+ "measurement set is to large.")
# *********************************************************************
# 3. if the npix from the parset is different to the ms calculations,
# calculate a sizeconverter value (to be applied to the cellsize)
if npix < 256:
self.logger.warn("Using a image size smaller then 256x256:"
" This leads to problematic imaging in some instances!!")
cell_size_formatted = str(
int(round(cell_size))) + 'arcsec'
self.logger.info("Using the following dynamic generated awimager parameters:"
" cell_size: {0}, npix: {1},".format(
cell_size_formatted, npix) +
" w_max: {0}, w_proj_planes: {1}".format(w_max, w_proj_planes))
# If we are not autocalculating based on ms or fov, use the npix
# and cell_size specified in the parset
# keep the wmax and w_proj_planes
if (not autogenerate_parameters and not specify_fov):
npix = parset_object.getString('npix')
cell_size = parset_object.getString('cellsize')
return cell_size_formatted, str(npix), str(w_max), str(w_proj_planes)
def run(self, executable, environment, parset, working_directory,
output_image, concatenated_measurement_set, sourcedb_path,
mask_patch_size, autogenerate_parameters, specify_fov, fov,
major_cycle, nr_cycles, perform_self_cal):
"""
:param executable: Path to awimager executable
:param environment: environment for catch_segfaults (executable runner)
:param parset: parameters for the awimager,
:param working_directory: directory the place temporary files
:param output_image: location and filesname to story the output images
the multiple images are appended with type extentions
:param concatenated_measurement_set: Input measurement set
:param sourcedb_path: Path the the sourcedb used to create the image
mask
:param mask_patch_size: Scaling of the patch around the source in the
mask
:param autogenerate_parameters: Turns on the autogeneration of:
cellsize, npix, wprojplanes, wmax, fov
:param fov: if autogenerate_parameters is false calculate
imageparameter (cellsize, npix, wprojplanes, wmax) relative to this
fov
:param major_cycle: number of the self calibration cycle to determine
the imaging parameters: cellsize, npix, wprojplanes, wmax, fov
:param nr_cycles: The requested number of self cal cycles
:param perform_self_cal: Bool used to control the selfcal functionality
or the old semi-automatic functionality
:rtype: self.outputs["image"] The path to the output image
"""
self.logger.info("Start selfcal_awimager node run:")
log4_cplus_name = "selfcal_awimager"
self.environment.update(environment)
with log_time(self.logger):
# Read the parameters as specified in the parset
parset_object = get_parset(parset)
# *************************************************************
# 1. Calculate awimager parameters that depend on measurement set
# and the parset
if perform_self_cal:
# Calculate awimager parameters that depend on measurement set
# and the parset
self.logger.info(
"Calculating selfcalibration parameters ")
cell_size, npix, w_max, w_proj_planes, \
UVmin, UVmax, robust, threshold =\
self._get_selfcal_parameters(
concatenated_measurement_set,
parset, major_cycle, nr_cycles)
self._save_selfcal_info(concatenated_measurement_set,
major_cycle, npix, UVmin, UVmax)
else:
self.logger.info(
"Calculating parameters.. ( NOT selfcalibration)")
cell_size, npix, w_max, w_proj_planes = \
self._get_imaging_parameters(
concatenated_measurement_set,
parset,
autogenerate_parameters,
specify_fov,
fov)
self.logger.info("Using autogenerated parameters; ")
self.logger.info(
"Calculated parameters: cell_size: {0}, npix: {1}".format(
cell_size, npix))
self.logger.info("w_max: {0}, w_proj_planes: {1} ".format(
w_max, w_proj_planes))
# ****************************************************************
# 2. Get the target image location from the mapfile for the parset.
# Create target dir if it not exists
image_path_head = os.path.dirname(output_image)
create_directory(image_path_head)
self.logger.debug("Created directory to place awimager output"
" files: {0}".format(image_path_head))
# ****************************************************************
# 3. Create the mask
#mask_file_path = self._create_mask(npix, cell_size, output_image,
# concatenated_measurement_set, executable,
# working_directory, log4_cplus_name, sourcedb_path,
# mask_patch_size, image_path_head)
# *****************************************************************
# 4. Update the parset with calculated parameters, and output image
patch_dictionary = {'uselogger': 'True', # enables log4cpluscd log
'ms': str(concatenated_measurement_set),
'cellsize': str(cell_size),
'npix': str(npix),
'wmax': str(w_max),
'wprojplanes': str(w_proj_planes),
'image': str(output_image),
'maxsupport': str(npix)
# 'mask':str(mask_file_path), #TODO REINTRODUCE
# MASK, excluded to speed up in this debug stage
}
# Add some aditional keys from the self calibration method
if perform_self_cal:
self_cal_patch_dict = {
'weight': 'briggs',
'padding': str(1.18),
'niter' : str(1000000),
'operation' : 'mfclark',
'timewindow' : '300',
'fits' : '',
'threshold' : str(threshold),
'robust' : str(robust),
'UVmin' : str(UVmin),
'UVmax' : str(UVmax),
'maxbaseline' : str(10000000),
'select' : str("sumsqr(UVW[:2])<1e12"),
}
patch_dictionary.update(self_cal_patch_dict)
# save the parset at the target dir for the image
calculated_parset_path = os.path.join(image_path_head,
"parset.par")
try:
temp_parset_filename = patch_parset(parset, patch_dictionary)
# Copy tmp file to the final location
shutil.copyfile(temp_parset_filename, calculated_parset_path)
self.logger.debug("Wrote parset for awimager run: {0}".format(
calculated_parset_path))
finally:
# remove temp file
os.remove(temp_parset_filename)
# *****************************************************************
# 5. Run the awimager with the parameterset
cmd = [executable, calculated_parset_path]
self.logger.debug("Parset used for awimager run:")
self.logger.debug(cmd)
try:
with CatchLog4CPlus(working_directory,
self.logger.name + "." +
os.path.basename(log4_cplus_name),
os.path.basename(executable)
) as logger:
catch_segfaults(cmd, working_directory, self.environment,
logger, usageStats=self.resourceMonitor)
# Thrown by catch_segfault
except CalledProcessError as exception:
self.logger.error(str(exception))
return 1
except Exception as exception:
self.logger.error(str(exception))
return 1
# *********************************************************************
# 6. Return output
# Append static .restored: This might change but prob. not
# The actual output image has this extention always, default of
# awimager
self.outputs["image"] = output_image + ".restored"
return 0
def _get_imaging_parameters(self, measurement_set, parset,
autogenerate_parameters, specify_fov, fov):
"""
(1) calculate and format some parameters that are determined runtime.
Based on values in the measurementset and input parameter (set):
a. <string> The cellsize
b. <int> The npixels in a each of the two dimension of the image
c. <string> The largest baseline in the ms smaller then the maxbaseline
d. <string> The number of projection planes
The calculation of these parameters is done in three steps:
1. Calculate intermediate results based on the ms.
2. The calculation of the actual target values using intermediate
result
"""
# *********************************************************************
# 1. Get partial solutions from the parameter set
# Get the parset and a number of raw parameters from this parset
parset_object = get_parset(parset)
baseline_limit = parset_object.getInt('maxbaseline')
# Get the longest baseline
max_baseline = pt.taql(
'CALC sqrt(max([select sumsqr(UVW[:2]) from ' + \
'{0} where sumsqr(UVW[:2]) <{1} giving as memory]))'.format(\
measurement_set, baseline_limit *
baseline_limit))[0] # ask ger van diepen for details if ness.
# Calculate the wave_length
table_ms = pt.table(measurement_set)
table_spectral_window = pt.table(
table_ms.getkeyword("SPECTRAL_WINDOW"))
freq = table_spectral_window.getcell("REF_FREQUENCY", 0)
table_spectral_window.close()
wave_length = pt.taql('CALC C()') / freq
wave_length = wave_length[0]
# Calculate the cell_size from the ms
arc_sec_in_degree = 3600
arc_sec_in_rad = (180.0 / math.pi) * arc_sec_in_degree
cell_size = (1.0 / 3) * (wave_length / float(max_baseline))\
* arc_sec_in_rad
# Calculate the number of pixels in x and y dim
# fov and diameter depending on the antenna name
fov_from_ms, station_diameter = self._get_fov_and_station_diameter(
measurement_set)
# use fov for to calculate a semi 'user' specified npix and cellsize
# The npix thus depends on the ms cellsize and fov
# Do not use use supplied Fov if autogenerating
if not autogenerate_parameters and specify_fov:
if fov == 0.0:
raise PipelineException("fov set to 0.0: invalid value.")
# else use full resolution (calculate the fov)
else:
self.logger.info("Using fov calculated on measurement data: " +
str(fov_from_ms))
fov = fov_from_ms
# ********************************************************************
# 2. Calculate the ms based output variables
# 'optimal' npix based on measurement set calculations or user specified
npix = (arc_sec_in_degree * fov) / cell_size
# Get the closest power of two larger then the calculated pixel size
npix = self._nearest_ceiled_power2(npix)
# Get the max w with baseline < 10000
w_max = pt.taql('CALC max([select UVW[2] from ' + \
'{0} where sumsqr(UVW[:2]) <{1} giving as memory])'.format(
measurement_set, baseline_limit * baseline_limit))[0]
# Calculate number of projection planes
w_proj_planes = min(257, math.floor((max_baseline * wave_length) /
(station_diameter ** 2)))
w_proj_planes = int(round(w_proj_planes))
# MAximum number of proj planes set to 1024: George Heald, Ger van
# Diepen if this exception occurs
maxsupport = max(1024, npix)
if w_proj_planes > maxsupport:
raise Exception("The number of projections planes for the current"
+ "measurement set is to large.")
# *********************************************************************
# 3. if the npix from the parset is different to the ms calculations,
# calculate a sizeconverter value (to be applied to the cellsize)
if npix < 256:
self.logger.warn("Using a image size smaller then 256x256:"
" This leads to problematic imaging in some instances!!")
# If we are not autocalculating based on ms or fov, use the npix
# and cell_size specified in the parset
# keep the wmax and w_proj_planes
if (not autogenerate_parameters and not specify_fov):
npix = parset_object.getString('npix')
cell_size_formatted = parset_object.getString('cellsize')
else:
cell_size_formatted = str(
int(round(cell_size))) + 'arcsec'
self.logger.info("Using the following awimager parameters:"
" cell_size: {0}, npix: {1},".format(
cell_size_formatted, npix) +
" w_max: {0}, w_proj_planes: {1}".format(w_max, w_proj_planes))
return cell_size_formatted, str(npix), str(w_max), str(w_proj_planes)
def run(self, executable, environment, parset, working_directory,
output_image, concatenated_measurement_set, sourcedb_path,
mask_patch_size, autogenerate_parameters, specify_fov, fov,
major_cycle, nr_cycles, perform_self_cal):
"""
:param executable: Path to awimager executable
:param environment: environment for catch_segfaults (executable runner)
:param parset: parameters for the awimager,
:param working_directory: directory the place temporary files
:param output_image: location and filesname to story the output images
the multiple images are appended with type extentions
:param concatenated_measurement_set: Input measurement set
:param sourcedb_path: Path the the sourcedb used to create the image
mask
:param mask_patch_size: Scaling of the patch around the source in the
mask
:param autogenerate_parameters: Turns on the autogeneration of:
cellsize, npix, wprojplanes, wmax, fov
:param fov: if autogenerate_parameters is false calculate
imageparameter (cellsize, npix, wprojplanes, wmax) relative to this
fov
:param major_cycle: number of the self calibration cycle to determine
the imaging parameters: cellsize, npix, wprojplanes, wmax, fov
:param nr_cycles: The requested number of self cal cycles
:param perform_self_cal: Bool used to control the selfcal functionality
or the old semi-automatic functionality
:rtype: self.outputs["image"] The path to the output image
"""
self.logger.info("Start selfcal_awimager node run:")
log4_cplus_name = "selfcal_awimager"
self.environment.update(environment)
with log_time(self.logger):
# Read the parameters as specified in the parset
parset_object = get_parset(parset)
# *************************************************************
# 1. Calculate awimager parameters that depend on measurement set
# and the parset
if perform_self_cal:
# Calculate awimager parameters that depend on measurement set
# and the parset
self.logger.info(
"Calculating selfcalibration parameters ")
cell_size, npix, w_max, w_proj_planes, \
UVmin, UVmax, robust, threshold =\
self._get_selfcal_parameters(
concatenated_measurement_set,
parset, major_cycle, nr_cycles)
self._save_selfcal_info(concatenated_measurement_set,
major_cycle, npix, UVmin, UVmax)
else:
self.logger.info(
"Calculating parameters.. ( NOT selfcalibration)")
cell_size, npix, w_max, w_proj_planes = \
self._get_imaging_parameters(
concatenated_measurement_set,
parset,
autogenerate_parameters,
specify_fov,
fov)
self.logger.info("Using autogenerated parameters; ")
self.logger.info(
"Calculated parameters: cell_size: {0}, npix: {1}".format(
cell_size, npix))
self.logger.info("w_max: {0}, w_proj_planes: {1} ".format(
w_max, w_proj_planes))
# ****************************************************************
# 2. Get the target image location from the mapfile for the parset.
# Create target dir if it not exists
image_path_head = os.path.dirname(output_image)
create_directory(image_path_head)
self.logger.debug("Created directory to place awimager output"
" files: {0}".format(image_path_head))
# ****************************************************************
# 3. Create the mask
#mask_file_path = self._create_mask(npix, cell_size, output_image,
# concatenated_measurement_set, executable,
# working_directory, log4_cplus_name, sourcedb_path,
# mask_patch_size, image_path_head)
# *****************************************************************
# 4. Update the parset with calculated parameters, and output image
patch_dictionary = {'uselogger': 'True', # enables log4cpluscd log
'ms': str(concatenated_measurement_set),
'cellsize': str(cell_size),
'npix': str(npix),
'wmax': str(w_max),
'wprojplanes': str(w_proj_planes),
'image': str(output_image),
'maxsupport': str(npix)
# 'mask':str(mask_file_path), #TODO REINTRODUCE
# MASK, excluded to speed up in this debug stage
}
# Add some aditional keys from the self calibration method
if perform_self_cal:
self_cal_patch_dict = {
'weight': 'briggs',
'padding': str(1.18),
'niter' : str(1000000),
'operation' : 'mfclark',
'timewindow' : '300',
'fits' : '',
'threshold' : str(threshold),
'robust' : str(robust),
'UVmin' : str(UVmin),
'UVmax' : str(UVmax),
'maxbaseline' : str(10000000),
'select' : str("sumsqr(UVW[:2])<1e12"),
}
patch_dictionary.update(self_cal_patch_dict)
# save the parset at the target dir for the image
calculated_parset_path = os.path.join(image_path_head,
"parset.par")
try:
temp_parset_filename = patch_parset(parset, patch_dictionary)
# Copy tmp file to the final location
shutil.copyfile(temp_parset_filename, calculated_parset_path)
self.logger.debug("Wrote parset for awimager run: {0}".format(
calculated_parset_path))
finally:
# remove temp file
os.remove(temp_parset_filename)
# *****************************************************************
# 5. Run the awimager with the parameterset
cmd = [executable, calculated_parset_path]
self.logger.debug("Parset used for awimager run:")
self.logger.debug(cmd)
try:
with CatchLog4CPlus(working_directory,
self.logger.name + "." +
os.path.basename(log4_cplus_name),
os.path.basename(executable)
) as logger:
catch_segfaults(cmd, working_directory, self.environment,
logger, usageStats=self.resourceMonitor)
# Thrown by catch_segfault
except CalledProcessError, exception:
self.logger.error(str(exception))
return 1
except Exception, exception:
self.logger.error(str(exception))
return 1
def run(self, executable, environment, parset, working_directory,
output_image, concatenated_measurement_set, sourcedb_path,
mask_patch_size, autogenerate_parameters, specify_fov, fov):
"""
:param executable: Path to awimager executable
:param environment: environment for catch_segfaults (executable runner)
:param parset: parameters for the awimager,
:param working_directory: directory the place temporary files
:param output_image: location and filesname to story the output images
the multiple images are appended with type extentions
:param concatenated_measurement_set: Input measurement set
:param sourcedb_path: Path the the sourcedb used to create the image
mask
:param mask_patch_size: Scaling of the patch around the source in the
mask
:param autogenerate_parameters: Turns on the autogeneration of:
cellsize, npix, wprojplanes, wmax, fov
:param fov: if autogenerate_parameters is false calculate
imageparameter (cellsize, npix, wprojplanes, wmax) relative to this
fov
:rtype: self.outputs["image"] The path to the output image
"""
self.logger.info("Start imager_awimager node run:")
log4_cplus_name = "imager_awimager"
self.environment.update(environment)
with log_time(self.logger):
# Read the parameters as specified in the parset
parset_object = get_parset(parset)
#******************************************************************
# 0. Create the directories used in this recipe
create_directory(working_directory)
# *************************************************************
# 1. Calculate awimager parameters that depend on measurement set
# and the parset
cell_size, npix, w_max, w_proj_planes = \
self._get_imaging_parameters(
concatenated_measurement_set,
parset,
autogenerate_parameters,
specify_fov,
fov)
self.logger.info("Using autogenerated parameters; ")
self.logger.info(
"Calculated parameters: cell_size: {0}, npix: {1}".format(
cell_size, npix))
self.logger.info("w_max: {0}, w_proj_planes: {1} ".format(
w_max, w_proj_planes))
# ****************************************************************
# 2. Get the target image location from the mapfile for the parset.
# Create target dir if it not exists
image_path_head = os.path.dirname(output_image)
create_directory(image_path_head)
self.logger.debug("Created directory to place awimager output"
" files: {0}".format(image_path_head))
# ****************************************************************
# 3. Create the mask
mask_file_path = self._create_mask(npix, cell_size, output_image,
concatenated_measurement_set,
executable, working_directory,
log4_cplus_name, sourcedb_path,
mask_patch_size,
image_path_head)
# *****************************************************************
# 4. Update the parset with calculated parameters, and output image
patch_dictionary = {
'uselogger': 'True', # enables log4cpluscd log
'ms': str(concatenated_measurement_set),
'cellsize': str(cell_size),
'npix': str(npix),
'wmax': str(w_max),
'wprojplanes': str(w_proj_planes),
'image': str(output_image),
'maxsupport': str(npix),
# 'mask':str(mask_file_path), #TODO REINTRODUCE
# MASK, excluded to speed up in this debug stage
}
# save the parset at the target dir for the image
calculated_parset_path = os.path.join(image_path_head,
"parset.par")
try:
temp_parset_filename = patch_parset(parset, patch_dictionary)
# Copy tmp file to the final location
shutil.copyfile(temp_parset_filename, calculated_parset_path)
self.logger.debug("Wrote parset for awimager run: {0}".format(
calculated_parset_path))
finally:
# remove temp file
os.remove(temp_parset_filename)
# *****************************************************************
# 5. Run the awimager with the updated parameterset
cmd = [executable, calculated_parset_path]
try:
with CatchLog4CPlus(
working_directory, self.logger.name + "." +
os.path.basename(log4_cplus_name),
os.path.basename(executable)) as logger:
catch_segfaults(cmd,
working_directory,
self.environment,
logger,
usageStats=self.resourceMonitor)
# Thrown by catch_segfault
except CalledProcessError, exception:
self.logger.error(str(exception))
return 1
except Exception, exception:
self.logger.error(str(exception))
return 1
