def format_sushibar(ftype_data, sobj_name=None):
if not sobj_name in ftype_data.raw_data:
return
data = ftype_data.raw_data[sobj_name]
# data = np.nan_to_num(ftype_data.raw_data[sobj_name])
header = ftype_data.header
af3 = np.array([i for i in data if np.isnan(i[header.index('par2')])])
data = np.array([i for i in data if not np.isnan(i[header.index('par2')])])
# GENERATE RockPy Data object for data
data = RockPy3.Data(data=data, column_names=list(map(str.lower, header)))
data.rename_column('m', 'mag')
data.rename_column('meas. time', 'time')
data.define_alias('m', ('x', 'y', 'z'))
if af3.any():
af3 = RockPy3.Data(data=af3, column_names=list(map(str.lower, header)))
af3.rename_column('m', 'mag')
af3.rename_column('meas. time', 'time')
af3.define_alias('m', ('x', 'y', 'z'))
else:
af3 = None
out = {'data': data,
'af3': af3}
return out
def __init__(self,
sobj,
mtype='mass',
fpath=None,
ftype='generic',
mass=1.0,
mass_unit='kg',
std=None,
time=None,
series=None,
**options):
super(Mass, self).__init__(sobj=sobj,
fpath=fpath,
ftype=ftype,
series=series,
**options)
mass_conversion = convert2(mass_unit, 'kg', 'mass')
if not mass_conversion:
self.log.warning(
'mass unit << %s >> most likely not mass-compatible' % unit)
self.log.error('CAN NOT create Measurement')
self.has_data = False
return
self._data = {
'data':
RockPy3.Data(column_names=['variable', 'mass', 'time', 'std_dev'])
}
self._data['data'][mtype] = mass * mass_conversion
self._data['data']['time'] = time
self._data['data']['std_dev'] = std
def format_jr6(ftype_data, sobj_name=None):
data = RockPy3.Data(data=ftype_data.data, column_names=ftype_data.header)
data.define_alias('m', ('x', 'y', 'z'))
data = data.append_columns(column_names='mag', data=data.magnitude(key='m'))
data = data.sort(key='variable')
out = {'data': data}
return out
def results(self):
results = RockPy3.Data(column_names='mID')
for i, mid in enumerate(self._raw_results):
if not 'mID' in self._raw_results[mid].column_names:
aux = self._raw_results[mid].append_columns(column_names='mID',
data=mid)
else:
aux = self._raw_results[mid]
results = results.append_rows(aux)
return results
def results(self):
results = RockPy3.Data(column_names='mID')
for s in sorted(self._raw_results):
for mid in self._raw_results[s]:
if not 'mID' in results.column_names:
aux = self._raw_results[s][mid].append_columns(
column_names='mID', data=mid)
else:
aux = self._raw_results[s][mid]
results = results.append_rows(aux)
return results
def __init__(self,
sobj,
mtype,
fpath=None,
ftype='combined',
height=None,
diameter=None,
sample_shape='cylinder',
x_len=None,
y_len=None,
z_len=None,
std=None,
time=None,
series=None,
**options):
super(Volume, self).__init__(sobj=sobj,
fpath=fpath,
ftype='combined',
**options)
self.sample_shape = sample_shape
volume = np.nan
if sample_shape == 'cylinder' and height and diameter:
height_data = height.data['data']['height'].v[0]
diameter_data = diameter.data['data']['diameter'].v[0]
volume = self.cylinder(height_data, diameter_data)
if x_len and y_len and z_len:
if sample_shape != 'cube': # check if all three dimensions but wrong/unset sample_shape
self.log.warning(
'sample_shape != cube \t but x_len, y_len, z_len provided -> assuming cube'
)
sample_shape = 'cube'
if sample_shape == 'cube':
x = x_len.data['data']['length'].v[0]
y = y_len.data['data']['length'].v[0]
z = z_len.data['data']['length'].v[0]
volume = self.cube(x, y, z)
if diameter and not height:
if sample_shape == 'sphere':
diameter_data = diameter.data['data']['diameter'].v[0]
volume = self.sphere(diameter_data)
# store in RockPy Data object
self._data = {
'data': RockPy3.Data(column_names=['volume', 'time', 'std_dev'])
}
self._data['data'][mtype] = volume
self._data['data']['time'] = time
self._data['data']['std_dev'] = std
def mean_results(self):
"""
Gives a RockPyData object with all results from mean measurements
Note:
does not average the results
Returns
-------
RockPyData
"""
results = RockPy3.Data(column_names='mID')
for i, mid in enumerate(self._raw_results):
aux = self._raw_mean_results[mid].append_columns(
column_names='mID', data=mid)
results = results.append_rows(aux)
return results
def format_sushibar(ftype_data, sobj_name=None):
if not sobj_name in ftype_data.raw_data:
return
data = np.nan_to_num(ftype_data.raw_data[sobj_name])
header = ftype_data.header
# data = np.array([i for i in data if not np.isnan(i[header.index('par2')])])
# print(data)
# GENERATE RockPy Data object for data
data = RockPy3.Data(data=data,
column_names=list(map(str.lower, header)))
data.rename_column('m', 'mag')
data.rename_column('meas. time', 'time')
data.define_alias('m', ('x', 'y', 'z'))
data.define_alias('variable', 'par1')
out = {
'data': data,
}
return out
def format_jr6(ftype_data, sobj_name=None):
"""
Import of a JR6 ftype_data object
Parameters
----------
ftype_data
sobj_name
Returns
-------
"""
data = RockPy3.Data(data=ftype_data.data,
column_names=ftype_data.header)
data.define_alias('m', ('x', 'y', 'z'))
data = data.append_columns(column_names='mag',
data=data.magnitude(key='m'))
data = data.sort()
data.define_alias('step', 'variable')
out = {'data': data}
return out
def format_cryomag(ftype_data, sobj_name=None):
if not sobj_name in ftype_data.raw_data:
RockPy3.logger.warning(
'CANT find sample name << {} >> in file'.format(sobj_name))
sobj_name = list(ftype_data.raw_data.keys())[0]
# raise ValueError('no sample named << {} >> in file'.format(sobj_name))
raw_data = ftype_data.raw_data[sobj_name]['stepdata']
header = ['step', 'D', 'I', 'M', 'X', 'Y', 'Z', 'a95', 'sM', 'time']
data = []
for d in raw_data:
aux = [d['step']]
aux_data = [d['results'][h] for h in header[1:]]
aux.extend(aux_data)
data.append(aux)
data = np.array(data).astype(float)
data = RockPy3.Data(data=data,
column_names=list(map(str.lower, header)))
data.rename_column('m', 'mag')
data.define_alias('m', ('x', 'y', 'z'))
data.define_alias('variable', 'step')
out = {'data': data}
return out
def __init__(self,
sobj,
fpath=None,
ftype='generic',
value=None,
unit='m',
direction=None,
std=None,
time=None,
series=None,
**options):
super(Length, self).__init__(sobj=sobj,
fpath=fpath,
ftype=ftype,
series=series,
**options)
if not value:
return
self.ftype = ftype
self.direction = direction
length_conversion = convert2(unit, 'm', 'length')
if not length_conversion:
self.log.warning('unit << %s >> most likely not %s-compatible' %
(unit, self.__class__.get_subclass_name()))
self.log.error('CAN NOT create Measurement')
self.has_data = False
return
self._data = {
'data': RockPy3.Data(column_names=[self.mtype, 'time', 'std_dev'])
}
self._data['data'][self.mtype] = value * length_conversion
self._data['data']['time'] = time
self._data['data']['std_dev'] = std
def wrapped_feature(*args, **kwargs):
# format the argspec
parameter = get_full_argspec(func=feature, args=args, kwargs=kwargs)
visual = parameter['self']
# update the plt_props of the feature
kwargs['plt_props'] = {}
name = kwargs.pop('name', '')
if self.single:
self.update_plt_props(kwargs, visual=visual, name=name)
self.plt_single_feature(feature=feature, visual=visual, **kwargs)
return wrapped_feature
############################################################################################################
# determine data parameters hierachically from fig -> visual -> feature
# meaning if only fig data, plot fig_input
# if fig_input and data -> fig_input is overwritten by data etc.
plt_info = self.get_plt_infos(feature=feature, visual=visual, name=name)
RockPy3.logger.debug('Input from:')
for k, v in sorted(plt_info.items()):
RockPy3.logger.debug(' {}:{}'.format(k, v))
############################################################################################################
# RESULT FEATURES
if self.result_feature:
"""
result feature uses either visual of feature plot_mean, plot_base and ignore_samples flags
if ignore_samples True: the mean of all samples_is calculated
False: the mean for each individual sample is plotted
"""
# cycle through possible inputs
data = {}
for plt_type in ('groupbase', 'samplebase', 'other', 'samplemean', 'groupmean'):
if plt_type not in plt_info:
continue
# skip everything that should not be plotted
if not plt_info['plot_' + plt_type]:
continue
# get the list of measurements
mlist = plt_info[plt_type]
# initialize plot properties
kwargs['plt_props'] = {}
# skip anything that has nothing to plot
if not mlist:
continue
# get rid of measurements without proper result and series
mlist = [m for m in mlist if m.has_result(visual.result) if m.get_series(stype=visual.series)]
# seaparate list into separate lists for each sample
# if ignore samples, all measurements will be used
if not plt_info['ignore_samples']:
samples = set(m.sobj.name for m in copy(mlist))
mlists = [tuple(m for m in mlist if m.sobj.name == sname) for sname in samples]
else:
mlists = [mlist]
# mlists is now a list of measurements for each sample
# iterate over the samples measurements
for mlist in mlists:
data.setdefault(plt_type, [])
# initialize the RPdata for each sample
sdata = RockPy3.Data(column_names=[visual.series, visual.result], row_names=[])
# calculate the results and get the series for all measurements
for m in mlist:
# get the sval of the specified series
sval = m.get_series(visual.series)[0].v
# calculate the result using the calculation parameters
res = getattr(m, 'result_' + visual.result)(**plt_info['calculation_parameter'])
d = RockPy3.Data(data=[sval, res[0]],
column_names=[visual.series, visual.result],
row_names='{}({})'.format(m.sobj.name, m.id))
sdata = sdata.append_rows(data=d)
# plot each individual result, append them to data
if 'base' in plt_type or plt_type == 'other':
kwargs['plt_props'] = deepcopy(m.plt_props)
# overwrite the plot properties of the measurement object if specified in the decorator
# e.g. for setting marker = '' in the hysteresis_data feature
self.update_plt_props(kwargs, visual=visual, name=name)
# update the plt_props for reducing the alpha
if (plt_type == 'samplebase' and plt_info['plot_samplemean'] and plt_info[
'samplemean']) or \
(plt_type == 'groupbase' and plt_info[
'plot_groupmean' and plt_info['groupmean']]):
kwargs['plt_props']['alpha'] = plt_info['base_alpha']
feature(visual, data=d, **kwargs)
else:
data[plt_type].append(sdata)
if plt_type == 'other' and plt_info['plot_samplemean']:
for i, sdata in enumerate(data['other']):
kwargs['plt_props'] = deepcopy(mlists[i][0].plt_props)
self.update_plt_props(kwargs, visual=visual, name=name)
sdata = sdata.eliminate_duplicate_variable_rows(substfunc='mean').sort()
# print(name)
# print(sdata)
feature(visual, data=sdata, **kwargs)
if 'mean' in plt_type:
mean_data = []
# if result_from_means: the results will be calculated from the data of any mean measurement
# that has been calculated beforand otherwise the mean of the results will be calculated
if not plt_info['result_from_means']:
base = plt_type.replace('mean', 'base')
for sdata in data[base]:
sdata = sdata.eliminate_duplicate_variable_rows(substfunc='mean').sort()
mean_data.append(sdata)
else:
for sdata in data[plt_type]:
sdata = sdata.eliminate_duplicate_variable_rows(substfunc='mean').sort()
mean_data.append(sdata)
# print(mean_data)
for sdata in mean_data:
# print(sdata)
kwargs['plt_props'] = {}
kwargs['plt_props'] = deepcopy(mlist[0].plt_props)
# overwrite the plot properties of the measurement object if specified in the decorator
# e.g. for setting marker = '' in the hysteresis_data feature
self.update_plt_props(kwargs, visual=visual, name=name)
kwargs['plt_props'].update({'alpha': 1, 'zorder': 100})
feature(visual, data=sdata, **kwargs)
############################################################################################################
# NORMAL FEATURES
else:
# cycle through possible inputs
for plt_type in ('groupmean', 'samplemean', 'groupbase', 'samplebase', 'other'):
# skip everything that should not be plotted
if not plt_info['plot_' + plt_type] or not plt_type in plt_info:
continue
# get the list of measurements
mlist = plt_info[plt_type]
# initialize plot properties
kwargs['plt_props'] = {}
if not mlist:
continue
# for visuals with several possible mtypes
for mtype in self.mtypes:
if type(mtype) == str:
mtype = (mtype,)
if len(mtype) > 1:
mobj = MlistToTupleList(mlist, mtype)
elif len(mtype) == 1:
mobj = [m for m in mlist if m.mtype == mtype[0]]
else:
visual.log.error(
'FEATURE {} data doesnt match mtype requirements {}'.format(feature.__name__,
mtype))
for mt_tuple in mobj:
try:
kwargs['plt_props'].update(mt_tuple[0].plt_props)
except TypeError:
kwargs['plt_props'].update(mt_tuple.plt_props)
# overwrite the plot properties of the measurement object if specified in the decorator
# e.g. for setting marker = '' in the hysteresis_data feature
kwargs = self.update_plt_props(kwargs, visual=visual, name=name)
for k in list(kwargs.keys()):
if k in kwargs['plt_props']:
kwargs.pop(k)
# change the alpha to base_alpha if group or sample base should be plotted and the means
if (plt_type == 'samplebase' and plt_info['plot_samplemean'] and plt_info['samplemean']) or \
(plt_type == 'groupbase' and plt_info['plot_groupmean'] and plt_info['groupmean']):
kwargs['plt_props']['alpha'] = plt_info['base_alpha']
if plt_type == 'groupmean':
kwargs['plt_props']['zorder'] = 100
if plt_type == 'samplemean':
kwargs['plt_props']['zorder'] = 50
feature(visual, mobj=mt_tuple, **kwargs)
