def loadPlasmaParams(filename=None, gui=True):
"""
Load plasma parameters.
Returns :class:`blowout.plasma.PlasmaParams`.
"""
if filename is None and gui:
import scisalt.qt as _ssqt
filename = _ssqt.getOpenFileName()
with _h5.File(name=filename, mode='r') as f:
_checkversion(f)
# ======================================
# Load metadata
# ======================================
mattrs = f['metadata'].attrs
xi_start = mattrs['xi_start']
xi_end = mattrs['xi_end']
dxi = mattrs['dxi']
np = mattrs['np']
# ======================================
# Create class
# ======================================
plasmaparams = PlasmaParams(
xi_start = xi_start,
xi_end = xi_end,
dxi = dxi,
np = np
)
return plasmaparams
def loadDrive(filename=None, gui=True):
if filename is None and gui:
import scisalt.qt as _ssqt
filename = _ssqt.getOpenFileName()
with _h5.File(name=filename, mode='r') as f:
_checkversion(f)
# ======================================
# Load metadata
# ======================================
mattrs = f['metadata'].attrs
sx = mattrs['sx']
sy = mattrs['sy']
sz = mattrs['sz']
charge = mattrs['charge']
gamma = mattrs['gamma']
return Drive(
sx = sx,
sy = sy,
sz = sz,
charge = charge,
gamma = gamma
)
def loadPlasmaIons(plasmaparams=None, filename=None, gui=True):
"""
Load plasma ions.
Returns :class:`blowout.ions.PlasmaIons`.
"""
if filename is None and gui:
import scisalt.qt as _ssqt
filename = _ssqt.getOpenFileName()
with _h5.File(name=filename, mode='r') as f:
_checkversion(f)
# ======================================
# Load metadata
# ======================================
mattrs = f['metadata'].attrs
# ======================================
# Load data
# ======================================
data = f['data']
img = _read_arrays(data, 'img')
bounds = _read_arrays(data, 'bounds')
closed_ellipse = _read_arrays(data, 'closed_ellipse')
xind = data['xind'].value
yind = data['yind'].value
results_flat = _read_dict(data, 'results_flat')
# ======================================
# Create class
# ======================================
plas = PlasmaIons(
PlasmaParams = plasmaparams,
)
# ======================================
# Put data into class
# ======================================
plas._img = img
plas._bounds = bounds
plas._closed_ellipse = closed_ellipse
plas._xind = xind
plas._yind = yind
plas._results_flat = results_flat
# # ======================================
# # Load coordinate data
# # ======================================
# plas.x_coords = x_coords
# plas.y_coords = y_coords
# plas.bx_coords = bx_coords
# plas.by_coords = by_coords
return plas
def loadPlasmaE(plasmaparams=None, filename=None, gui=True):
"""
Load plasma particles.
Returns :class:`blowout.electrons.PlasmaE`.
"""
if filename is None and gui:
import scisalt.qt as _ssqt
filename = _ssqt.getOpenFileName()
with _h5.File(name=filename, mode='r') as f:
_checkversion(f)
# ======================================
# Load metadata
# ======================================
mattrs = f['metadata'].attrs
num_parts = mattrs['num_parts']
# ======================================
# Load data
# ======================================
data = f['data']
x_coords = data['x_coords'].value
y_coords = data['y_coords'].value
bx_coords = data['bx_coords'].value
by_coords = data['by_coords'].value
# ======================================
# Create class
# ======================================
plas = PlasmaE(
PlasmaParams = plasmaparams,
num_parts = num_parts,
)
# ======================================
# Load coordinate data
# ======================================
plas.x_coords = x_coords
plas.y_coords = y_coords
plas.bx_coords = bx_coords
plas.by_coords = by_coords
return plas
def get_valid_filename(pathstr, experiment, verbose=False, local=False):
# File doesn't exist
# This case must terminate in us trying again.
logger.log(level=loggerlevel, msg='Input is: pathstr={}'.format(pathstr))
# ======================================
# Return info if the file is local
# ======================================
if local:
if not _path.exists(pathstr):
_warnings.warn('File not found: {}'.format(pathstr))
# raise IOError('File not found: {}'.format(pathstr))
pathstr = _path.abspath(pathstr)
dir_beg = ''
dir_mid = _path.dirname(pathstr)
filename = _path.basename(pathstr)
data_source_type = '2014'
output = (dir_beg, dir_mid, filename, data_source_type)
return output
# ======================================
# Return info if the file is a nas file
# ======================================
if not _path.exists(pathstr):
logger.log(level=loggerlevel,
msg='Path does not exist: {}'.format(pathstr))
# If file didn't exist, maybe it needs a prefix
# Append prefix
prefix = get_remoteprefix()
pathstr = _path.join(prefix, pathstr)
# print(prefix)
# If it didn't work, we need to find the file somehow
# The prefix may be wrong, the file may not be where we thought,
# or the drive might not have been mounted and we can mount and
# try again.
if not _path.exists(pathstr):
logger.log(level=loggerlevel,
msg='Adding prefix didn'
't help, new pathstr={}'.format(pathstr))
title = 'File not found!'
maintext = 'File doesn' 't exist:\n\n{}'.format(pathstr)
subtext = '(External drive may not be mounted.)'
buttons = _np.array([
_mtqt.Button('Try again', _QtGui.QMessageBox.AcceptRole),
_mtqt.Button('Change prefix',
_QtGui.QMessageBox.ActionRole,
default=True),
_mtqt.Button('Locate file', _QtGui.QMessageBox.ActionRole),
_QtGui.QMessageBox.Abort
])
buttonbox = _mtqt.ButtonMsg(maintext,
title=title,
infotext=subtext,
buttons=buttons)
clicked = buttonbox.clickedArray
# Change prefix
if clicked[0]:
logger.log(level=loggerlevel, msg='Trying again')
elif clicked[1]:
logger.log(level=loggerlevel, msg='Changing prefix')
prefix = choose_remoteprefix(pathstart=prefix)
# Locate file
elif clicked[2]:
logger.log(level=loggerlevel, msg='Locating file')
# Try to open the path by chopping of the end
while not _path.isdir(pathstr):
lastpath = pathstr
pathstr = _path.dirname(pathstr)
# If you've chopped all you can chop, look in the base data folder
if lastpath == pathstr:
pathstr = _get_datapath()
break
pathstr = _mtqt.getOpenFileName(directory=pathstr,
caption='Locate file',
filter='Matlab Files (*.mat)')
elif clicked[3]:
logger.log(level=loggerlevel, msg='Aborting')
raise IOError('Aborting')
else:
print('Thar be dragons!')
logger.log(level=loggerlevel,
msg='Trying new pathstr={}'.format(pathstr))
return get_valid_filename(pathstr)
elif _path.isdir(pathstr):
logger.log(level=loggerlevel, msg='Path is a directory')
patterns = [
'*scan_info.mat', '*filenames.mat', '{}_*.mat'.format(experiment)
]
files = _np.array([])
for i, val in enumerate(patterns):
gfiles = _glob(_path.join(pathstr, val))
files = _np.append(files, gfiles)
logger.log(level=loggerlevel,
msg='Files match patterns\npatterns: {}\nfiles: {}'.format(
patterns, files))
if files.size == 1:
logger.log(level=loggerlevel, msg='Found one file.')
pathstr = files[0]
elif files.size == 0:
logger.log(level=loggerlevel, msg='Found no files.')
title = 'File Not Found'
maintext = 'No valid file found in folder.'
subtext = 'Locate manually?'
buttons = _np.array(
[_QtGui.QMessageBox.Ok, _QtGui.QMessageBox.Abort],
dtype=object)
buttonbox = _mtqt.ButtonMsg(maintext,
title=title,
infotext=subtext,
buttons=buttons)
clicked = buttonbox.clickedArray
if clicked[0]:
logger.log(level=loggerlevel, msg='Trying to locate manually.')
pathstr = _mtqt.getOpenFileName(directory=pathstr,
caption='Locate file',
filter='Matlab Files (*.mat)')
elif clicked[1]:
logger.log(level=loggerlevel, msg='Aborting.')
raise IOError('Aborting')
logger.log(level=loggerlevel,
msg='Trying new pathstr={}'.format(pathstr))
return get_valid_filename(pathstr)
elif _path.isfile(pathstr):
logger.log(level=loggerlevel, msg='Path is a file.')
# Check for string endings
strends = _np.array([
'scan_info.mat$', 'filenames.mat$',
'{}_[0-9]*\.mat'.format(experiment)
])
strmatch = _np.empty(strends.size, dtype=object)
for i, val in enumerate(strends):
strmatch[i] = _re.search(val, pathstr)
# True for matches
strmatch_bool = _np.not_equal(strmatch, None)
# Warn if there are no matches
if not _np.any(strmatch_bool):
logger.log(level=loggerlevel,
msg='File doesn'
't match patterns={}'.format(strends))
_warnings.warn(
'Neither a 2014+ data file, scan_info.mat file, nor a filenames.mat file: {}'
.format(pathstr))
if strmatch_bool[2]:
data_source_type = '2014'
else:
data_source_type = '2013'
logger.log(level=loggerlevel,
msg='data_source_type is {}'.format(data_source_type))
# Check that this is a data file
# Must have /nas/nas-li20-pm01
match = _re.search('/nas/nas-li20-pm0', pathstr)
if match is None:
raise IOError(
'Does not point to a file with /nas/nas-li20-pm01 or /nas/nas-li20-pm00 in its path.'
)
# Get the directories
dirstr = _path.dirname(pathstr)
filename = _path.basename(pathstr)
dir_beg = dirstr[:match.start()]
dir_mid = dirstr[match.start() + 1:]
output = (dir_beg, dir_mid, filename, data_source_type)
logger.log(level=loggerlevel, msg='Output is: {}'.format(output))
return output
def get_valid_filename(pathstr, experiment, verbose=False, local=False):
# File doesn't exist
# This case must terminate in us trying again.
logger.log(level=loggerlevel, msg='Input is: pathstr={}'.format(pathstr))
# ======================================
# Return info if the file is local
# ======================================
if local:
if not _path.exists(pathstr):
_warnings.warn('File not found: {}'.format(pathstr))
# raise IOError('File not found: {}'.format(pathstr))
pathstr = _path.abspath(pathstr)
dir_beg = ''
dir_mid = _path.dirname(pathstr)
filename = _path.basename(pathstr)
data_source_type = '2014'
output = (dir_beg, dir_mid, filename, data_source_type)
return output
# ======================================
# Return info if the file is a nas file
# ======================================
if not _path.exists(pathstr):
logger.log(level=loggerlevel, msg='Path does not exist: {}'.format(pathstr))
# If file didn't exist, maybe it needs a prefix
# Append prefix
prefix = get_remoteprefix()
pathstr = _path.join(prefix, pathstr)
# print(prefix)
# If it didn't work, we need to find the file somehow
# The prefix may be wrong, the file may not be where we thought,
# or the drive might not have been mounted and we can mount and
# try again.
if not _path.exists(pathstr):
logger.log(level=loggerlevel, msg='Adding prefix didn''t help, new pathstr={}'.format(pathstr))
title = 'File not found!'
maintext = 'File doesn''t exist:\n\n{}'.format(pathstr)
subtext = '(External drive may not be mounted.)'
buttons = _np.array([
_mtqt.Button('Try again', _QtGui.QMessageBox.AcceptRole),
_mtqt.Button('Change prefix', _QtGui.QMessageBox.ActionRole, default=True),
_mtqt.Button('Locate file', _QtGui.QMessageBox.ActionRole),
_QtGui.QMessageBox.Abort
])
buttonbox = _mtqt.ButtonMsg(maintext, title=title, infotext=subtext, buttons=buttons)
clicked = buttonbox.clickedArray
# Change prefix
if clicked[0]:
logger.log(level=loggerlevel, msg='Trying again')
elif clicked[1]:
logger.log(level=loggerlevel, msg='Changing prefix')
prefix = choose_remoteprefix(pathstart=prefix)
# Locate file
elif clicked[2]:
logger.log(level=loggerlevel, msg='Locating file')
# Try to open the path by chopping of the end
while not _path.isdir(pathstr):
lastpath = pathstr
pathstr = _path.dirname(pathstr)
# If you've chopped all you can chop, look in the base data folder
if lastpath == pathstr:
pathstr = _get_datapath()
break
pathstr = _mtqt.getOpenFileName(directory=pathstr, caption='Locate file', filter='Matlab Files (*.mat)')
elif clicked[3]:
logger.log(level=loggerlevel, msg='Aborting')
raise IOError('Aborting')
else:
print('Thar be dragons!')
logger.log(level=loggerlevel, msg='Trying new pathstr={}'.format(pathstr))
return get_valid_filename(pathstr)
elif _path.isdir(pathstr):
logger.log(level=loggerlevel, msg='Path is a directory')
patterns = ['*scan_info.mat', '*filenames.mat', '{}_*.mat'.format(experiment)]
files = _np.array([])
for i, val in enumerate(patterns):
gfiles = _glob(_path.join(pathstr, val))
files = _np.append(files, gfiles)
logger.log(level=loggerlevel, msg='Files match patterns\npatterns: {}\nfiles: {}'.format(patterns, files))
if files.size == 1:
logger.log(level=loggerlevel, msg='Found one file.')
pathstr = files[0]
elif files.size == 0:
logger.log(level=loggerlevel, msg='Found no files.')
title = 'File Not Found'
maintext = 'No valid file found in folder.'
subtext = 'Locate manually?'
buttons = _np.array([
_QtGui.QMessageBox.Ok,
_QtGui.QMessageBox.Abort
], dtype=object)
buttonbox = _mtqt.ButtonMsg(maintext, title=title, infotext=subtext, buttons=buttons)
clicked = buttonbox.clickedArray
if clicked[0]:
logger.log(level=loggerlevel, msg='Trying to locate manually.')
pathstr = _mtqt.getOpenFileName(directory=pathstr, caption='Locate file', filter='Matlab Files (*.mat)')
elif clicked[1]:
logger.log(level=loggerlevel, msg='Aborting.')
raise IOError('Aborting')
logger.log(level=loggerlevel, msg='Trying new pathstr={}'.format(pathstr))
return get_valid_filename(pathstr)
elif _path.isfile(pathstr):
logger.log(level=loggerlevel, msg='Path is a file.')
# Check for string endings
strends = _np.array(['scan_info.mat$', 'filenames.mat$', '{}_[0-9]*\.mat'.format(experiment)])
strmatch = _np.empty(strends.size, dtype=object)
for i, val in enumerate(strends):
strmatch[i] = _re.search(val, pathstr)
# True for matches
strmatch_bool = _np.not_equal(strmatch, None)
# Warn if there are no matches
if not _np.any(strmatch_bool):
logger.log(level=loggerlevel, msg='File doesn''t match patterns={}'.format(strends))
_warnings.warn('Neither a 2014+ data file, scan_info.mat file, nor a filenames.mat file: {}'.format(pathstr))
if strmatch_bool[2]:
data_source_type = '2014'
else:
data_source_type = '2013'
logger.log(level=loggerlevel, msg='data_source_type is {}'.format(data_source_type))
# Check that this is a data file
# Must have /nas/nas-li20-pm01
match = _re.search('/nas/nas-li20-pm0', pathstr)
if match is None:
raise IOError('Does not point to a file with /nas/nas-li20-pm01 or /nas/nas-li20-pm00 in its path.')
# Get the directories
dirstr = _path.dirname(pathstr)
filename = _path.basename(pathstr)
dir_beg = dirstr[:match.start()]
dir_mid = dirstr[match.start()+1:]
output = (dir_beg, dir_mid, filename, data_source_type)
logger.log(level=loggerlevel, msg='Output is: {}'.format(output))
return output