def test_add_measurement(self):
measurement = self.sample.add_measurement(
mtype='thellier',
mfile=self.cryomag_thellier_file,
machine='cryomag')
check = {
'nrm': [
2.00000000e+01, 2.08720000e-08, -8.95180000e-09,
5.04950000e-09, 2.88920000e-10, 735277.720278, 2.32652650e-08
],
}
for i in check:
for j, v in enumerate(check[i]):
self.assertAlmostEqual(measurement.data[i].v[0][j], v, 5)
path = join(
RockPy.test_data_path,
'LF4C-HX_1a_TT_CRY#320[mg]_5.17[mm]_5.84[mm]#pressure_1.2_GPa#.000'
)
print RockPy.get_fname_from_info(sample_group='LF4C-HX',
sample_name='1a',
mtype='TT',
machine='CRY',
mass=320,
mass_unit='mg',
height=5.17,
height_unit='mm',
diameter=5.87,
series='pressure',
svals=1.2,
sunits='GPa')
m = self.sample.add_measurement(path=path)
def test():
# define measurement data file
vftb_file = os.path.join(RockPy.test_data_path, 'vftb', 'MUCVFTB_test.coe')
# create a sample
sample = Sample(name='vftb_test_sample')
# add measurement
M = sample.add_measurement(mtype='backfield',
mfile=vftb_file,
machine='vftb',
suffix='test 1 none')
sg = RockPy.SampleGroup(sample_list=sample)
study = RockPy.Study(samplegroups=sg)
# get bcr
M.calculate_bcr(
) # prints the linear interpolation of the value (internal calculation)
print 'bcr', M.bcr # returns the calculated value
print M.s300 # returns the S300 value
M.calc_all() # calculates all possible results using standard parameters
print M.results # returns the calculated value
# rudimentary plot
M.plt_backfield()
sample.calc_all()
print sample.results
def import_folder(folder, name='study', study=None):
if not study:
study = RockPy.Study(name=name)
files = [
i for i in os.listdir(folder) if not i == '.DS_Store'
if not i.startswith('#')
]
samples = defaultdict(list)
for i in files:
d = RockPy.get_info_from_fname(join(folder, i))
samples[d['name']].append(d)
for s in samples:
sgroup_name = samples[s][0]['sample_group']
if not sgroup_name in study.samplegroup_names:
sg = RockPy.SampleGroup(name=samples[s][0]['sample_group'])
study.add_samplegroup(sg)
sg = study[sgroup_name]
if not s in study.sdict:
smpl = RockPy.Sample(**samples[s][0])
sg.add_samples(smpl)
for m in samples[s]:
measurement = smpl.add_measurement(**m)
if 'ISindex' in m:
initial = get_IS(m, samples[s])
measurement.set_initial_state(**initial)
samples[s].remove(initial)
if 'IS' in m and m['IS'] == True:
continue
return study
def test_add_m2_mdict(self):
sample = RockPy.Sample(name='test')
compare = deepcopy(sample.mdict)
m1 = RockPy.Measurement(sample_obj=sample,
mfile=None,
machine='generic',
mtype='mass',
mdata=[1])
m1.add_sval(stype='m1a', sval=1)
m1.add_sval(stype='m1b', sval=2)
sample.add_m2_mdict(mobj=m1)
self.assertTrue(m1 in sample.mdict['stype']['m1a'])
self.assertTrue(m1 in sample.mdict['stype']['m1b'])
m2 = RockPy.Measurement(sample_obj=sample,
mfile=None,
machine='generic',
mtype='height',
mdata=[1])
m2.add_sval(stype='m2a', sval=3)
m2.add_sval(stype='m2b', sval=4)
self.assertTrue(m2 in sample.mdict['stype']['m2a'])
self.assertTrue(m2 in sample.mdict['stype']['m2b'])
m2.add_sval(stype='m2c-added_later', sval=100)
self.assertTrue(m2 in sample.mdict['stype']['m2c-added_later'])
sample.remove_m_from_mdict(mobj=m1)
self.assertFalse('m1a' in sample.mdict['stype'])
self.assertFalse('m1b' in sample.mdict['stype'])
sample.remove_m_from_mdict(mobj=m2)
self.assertDictEqual(compare, sample.mdict)
def get_hys_coe_irm_rmp_sample_group(load=False):
if load:
study = RockPy.load(file_name='hys_coe_irm_rmp.rpy')
SG = study[0]
else:
S = sample.get_hys_coe_irm_rmp_sample()
SG = RockPy.SampleGroup(name='hys/coe/irm/rmp', sample_list=S)
study = RockPy.Study(SG)
RockPy.save(study, file_name='hys_coe_irm_rmp.rpy')
return SG
def setUp(self):
vsm_file = '../tutorials.rst/test_data/MUCVSM_test.hys'
# vsm_file = join(RockPy.test_data_path, 'vsm', 'LTPY_527,1a_HYS_VSM#XX[mg]___#TEMP_300_K#STD000.000')
self.sample = RockPy.Sample('test')
self.VSM_test = RockPy.Sample('test')
self.VSM_hys = self.VSM_test.add_measurement(mtype='hysteresis',
mfile=vsm_file,
machine='vsm')
self.simulation = self.sample.add_simulation(mtype='hysteresis',
mrs_ms=0.5,
ms=5.,
b_sat=0.8,
hf_sus=0)
def test_add_m2_info_dict(self):
sample = RockPy.Sample(name='test')
m = RockPy.Measurement(sample_obj=sample,
mfile=None,
machine='generic',
mtype='mass',
mdata=[1])
sample.add_measurement(mobj=m)
pprint(sample.info_dict)
sample2 = RockPy.Sample(name='test')
sample2.add_m2_info_dict(m)
sample2.add_m2_info_dict(m)
pprint(sample2.info_dict)
def setUp(self):
self.sample = RockPy.Sample(
name='test_sample',
mass=34.5,
mass_unit='mg',
diameter=5.4,
height=4.3,
length_unit='mm',
series='pressure_0.0_GPa; temperature_300.0_C')
self.cryomag_thellier_file = join(RockPy.test_data_path, 'cryomag',
'NLCRY_Thellier_test.TT')
self.cryomag_thellier_is_file = join(RockPy.test_data_path, 'cryomag',
'NLCRY_Thellier_is_test.TT')
# vftb
self.vftb_coe_file = join(RockPy.test_data_path, 'VFTB',
'MUCVFTB_test.coe')
self.vftb_hys_file = join(RockPy.test_data_path, 'VFTB',
'MUCVFTB_test.hys')
self.vftb_irm_file = join(RockPy.test_data_path, 'VFTB',
'MUCVFTB_test.irm')
self.vftb_rmp_file = join(RockPy.test_data_path, 'VFTB',
'MUCVFTB_test.rmp')
# vsm
self.vsm_hys_file = ''
self.vsm_hys_virgin_file = ''
self.vsm_hys_msi_file = ''
self.vsm_coe_file = ''
self.vsm_coe_irm_file = ''
self.vsm_coe_irm_induced_file = ''
self.vsm_rmp_file = ''
def test_add_samplegroup(self):
study = RockPy.Study(samplegroups=self.sample_group)
self.assertEqual(1, len(study.samplegroups))
# add second sample_group
study.add_samplegroup(self.sample_group)
# adding two sample_groups should make three sample_groups because all_samplegroup is added automatically
self.assertEqual(3, len(study.samplegroups))
def __init__(self,
sample_obj,
mtype,
mfile=None,
machine='generic',
value=1.0,
unit='m',
direction=None,
std=None,
time=None,
**options):
super(Length, self).__init__(sample_obj=sample_obj,
mtype=mtype,
mfile=mfile,
machine=machine,
**options)
self.mtype = mtype
self.machine = machine
self.direction = direction
length_conversion = convert2(unit, 'm', 'length')
self._raw_data = {
'data': RockPy.RockPyData(column_names=[mtype, 'time', 'std_dev'])
}
self._raw_data['data'][mtype] = value * length_conversion
self._raw_data['data']['time'] = time
self._raw_data['data']['std_dev'] = std
def test():
Sample = RockPy.Sample(name='parameter_test',
mass=10.,
mass_unit='kg',
height=4.5,
diameter=6.,
length_unit='mm')
Sample = RockPy.Sample(name='parameter_test',
mass=10.,
mass_unit='kg',
sample_shape='sphere',
x_len=4.5,
y_len=6.,
z_len=6.,
length_unit='mm')
print Sample.volume, Sample.mass
def import_folder(folder, name='study', study=None):
if not study:
study = RockPy.Study(name=name)
files = [i for i in os.listdir(folder) if not i == '.DS_Store' if not i.startswith('#')]
samples = defaultdict(list)
for i in files:
d = RockPy.get_info_from_fname(join(folder, i))
samples[d['name']].append(d)
for s in samples:
sgroup_name = samples[s][0]['sample_group']
if not sgroup_name in study.samplegroup_names:
sg = RockPy.SampleGroup(name=samples[s][0]['sample_group'])
study.add_samplegroup(sg)
sg = study[sgroup_name]
if not s in study.sdict:
smpl = RockPy.Sample(**samples[s][0])
sg.add_samples(smpl)
for m in samples[s]:
measurement = smpl.add_measurement(**m)
if 'ISindex' in m:
initial = get_IS(m, samples[s])
measurement.set_initial_state(**initial)
samples[s].remove(initial)
if 'IS' in m and m['IS'] == True:
continue
return study
def Arai():
S = RockPy.Tutorials.sample_group.get_thellier_samplegroup()
ST = RockPy.Study(S, name='TT-test-ST')
P = RockPy.Visualize.paleointensity.Arai(ST)
P.add_all_samples()
P.show()
def test():
vftb_file = 'test_data/MUCVFTB_test.hys'
vsm_file = 'test_data/MUCVSM_test.hys'
sample = RockPy.Sample(name='vftb_test_sample')
sample2 = RockPy.Sample(name='vsm_test_sample')
M = sample.add_measurement(mtype='hysteresis', mfile=vftb_file, machine='vftb')
M = sample2.add_measurement(mtype='hysteresis', mfile=vsm_file, machine='vsm')
study = RockPy.Study(samplegroups=[sample])
RockPy.save(study, file_name='test.rpy')
study2 = RockPy.load(file_name='test.rpy')
print study2
def get_sample_with_multiple_hys():
sample = RockPy.Sample(name='test_sample',
mass=34.5,
mass_unit='mg',
diameter=5.4,
height=4.3,
length_unit='mm',
series='pressure_0.0_GPa; temperature_300.0_C')
vftb_hys_file = join(RockPy.test_data_path, 'vftb', 'MUCVFTB_test.hys')
m1 = sample.add_measurement(mtype='hys',
machine='vftb',
mfile=vftb_hys_file,
series='pressure_0.0_GPa; temperature_100.0_C')
m2 = deepcopy(m1)
m3 = deepcopy(m2)
for dtype in m2.data:
for column in m2.data[dtype].column_names:
m2.data[dtype][column] = 0.1 + m2.data[dtype][column].v
for dtype in m3.data:
for column in m3.data[dtype].column_names:
m3.data[dtype][column] = 0.1 + m3.data[dtype][column].v
return sample
def test():
vftb_file = 'test_data/MUCVFTB_test.rmp'
sample = RockPy.Sample(name='vftb_test_sample')
M = sample.add_measurement(mtype='thermocurve',
mfile=vftb_file,
machine='vftb')
M.plt_thermocurve()
def test():
sample = RP.Sample(name='test_sample')
sample.add_measurement(
mtype='thellier',
mfile='../tutorials.rst/test_data/NLCRY_Thellier_test.TT',
machine='cryomag')
Plot = Arai(plot_samples=sample)
Plot.show()
def import_folderOLD(folder, name='study', study=None):
"""
imports a whole folder creating a study, sample_groups and samples
"""
if not study:
study = RockPy.Study(name=name)
# get all files in directory
files = [
i for i in os.listdir(folder) if not i == '.DS_Store'
if not i.startswith('#')
]
for f in files:
d = RockPy.get_info_from_fname(f, folder)
if 'IS' in d and d['IS']:
pass
if not d['sample_group'] in study.samplegroup_names:
sg = RockPy.SampleGroup(name=d['sample_group'])
study.add_samplegroup(sg)
else:
sg = study.gdict[d['sample_group']]
if not d['name'] in sg.sample_names:
s = RockPy.Sample(**d)
sg.add_samples(s)
else:
s = sg.get_samples(snames=d['name'])[0]
m = s.add_measurement(**d)
if 'ISindex' in d:
idx = [(i, f) for i, f in enumerate(files)
if d['ISindex'] in f.split('.')[-1]
if 'IS_True' in f] #initial_state index
if len(idx) > 1:
print 'more than one initial state found not adding any'
else:
initial = RockPy.get_info_from_fname(files[idx[0]], folder)
del files[idx[0]]
m.set_initial_state(**initial)
# print study
# print study.samplegroups
# print sg
# print sg.samples
# print s
return study
def get_af_demag_sample():
folder = RockPy.test_data_path
S = RockPy.Sample(name='WURM')
af = join(folder, 'MUCSUSH_af_test.af')
S.add_measurement(mtype='afdemag',
mfile=af,
machine='sushibar',
magtype='irm')
return S
def test():
import RockPy
from os.path import join
test_file = join(RockPy.test_data_path, 'MUCSUSH_af_test.af')
S = RockPy.Sample(name='WURM')
print S.add_measurement(mtype='afdemag',
mfile=test_file,
machine='sushibar')
def Day1977():
SG = RockPy.Tutorials.sample_group.get_hys_coe_irm_rmp_sample_group(
load=False)
ST = RockPy.Study(name='day_plot', samplegroups=SG)
S = SG.sample_list[0]
m = S.get_measurements('hysteresis')[0]
m.show_plots()
def test():
dfile = os.path.join(RockPy.test_data_path, 'vftb', 'MUCVFTB_test.rmp')
sample = RockPy.Sample(name='vftb_test')
M = sample.add_measurement(mtype='thermocurve',
mfile=dfile,
machine='vftb')
M.plt_thermocurve()
def test():
vftb_file = 'test_data/MUCVFTB_test.irm'
sample = RockPy.Sample(name='vftb_test_sample')
M = sample.add_measurement(mtype='irm_acquisition',
mfile=vftb_file,
machine='vftb')
print list(M.data['remanence']['field'].v)
print list(M.data['remanence']['mag'].v)
def get_thellier_samplegroup():
folder = RockPy.test_data_path
sample_file = join(folder, 'sample_info.csv')
tt_data = join(folder, 'NLCRY_Thellier_test.TT')
SG = RockPy.SampleGroup(name='TT-test-SG')
SG.import_multiple_samples(sample_file=sample_file)
for sample in SG.sample_list:
M = sample.add_measurement(mtype='thellier', mfile=tt_data, machine='cryomag', series='p0')
return SG
def setUp(self):
self.sample = RockPy.Sample(name='test_sample')
# files
vsm_file = os.path.join(
RockPy.test_data_path, 'vsm',
'FeNi20_FeNi20-Ga72-G01_VISC_VSM#6,0[mg]_[]_[]###.001')
# add measurements
self.vsm_measurement = self.sample.add_measurement(mtype='viscosity',
mfile=vsm_file,
machine='vsm')
def import_folderOLD(folder, name='study', study=None):
"""
imports a whole folder creating a study, sample_groups and samples
"""
if not study:
study = RockPy.Study(name=name)
# get all files in directory
files = [i for i in os.listdir(folder) if not i == '.DS_Store' if not i.startswith('#')]
for f in files:
d = RockPy.get_info_from_fname(f, folder)
if 'IS' in d and d['IS']:
pass
if not d['sample_group'] in study.samplegroup_names:
sg = RockPy.SampleGroup(name=d['sample_group'])
study.add_samplegroup(sg)
else:
sg = study.gdict[d['sample_group']]
if not d['name'] in sg.sample_names:
s = RockPy.Sample(**d)
sg.add_samples(s)
else:
s = sg.get_samples(snames=d['name'])[0]
m = s.add_measurement(**d)
if 'ISindex'in d:
idx = [(i, f) for i, f in enumerate(files) if d['ISindex'] in f.split('.')[-1] if 'IS_True' in f] #initial_state index
if len(idx) >1:
print 'more than one initial state found not adding any'
else:
initial = RockPy.get_info_from_fname(files[idx[0]], folder)
del files[idx[0]]
m.set_initial_state(**initial)
# print study
# print study.samplegroups
# print sg
# print sg.samples
# print s
return study
def __init__(self,
sample_obj,
mtype,
mfile=None,
machine='combined',
height=None,
diameter=None,
sample_shape='cylinder',
x_len=None,
y_len=None,
z_len=None,
std=None,
time=None,
**options):
super(Volume, self).__init__(sample_obj=sample_obj,
mtype=mtype,
mfile=mfile,
machine='combined',
**options)
self.sample_shape = sample_shape
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.logger.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._raw_data = {
'data':
RockPy.RockPyData(column_names=['volume', 'time', 'std_dev'])
}
self._raw_data['data'][mtype] = volume
self._raw_data['data']['time'] = time
self._raw_data['data']['std_dev'] = std
def get_test_sample(recalc=False):
if os.path.isfile(join(RockPy.test_data_path, 'TTtest.rpy')) or recalc:
cryomag_file1 = join(RockPy.test_data_path, 'LF4C-HX_1a_TT_CRY#320[mg]_5.17[mm]_5.84[mm]#pressure_0.0_GPa#.000')
cryomag_file2 = join(RockPy.test_data_path, 'LF4C-HX_1a_TT_CRY#320[mg]_5.17[mm]_5.84[mm]#pressure_0.6_GPa#.000')
cryomag_file3 = join(RockPy.test_data_path, 'LF4C-HX_1a_TT_CRY#320[mg]_5.17[mm]_5.84[mm]#pressure_1.2_GPa#.000')
# creating a sample
sample = RockPy.Sample(name='1a')
# adding the measurement to the sample
M = sample.add_measurement(mtype='thellier', mfile=cryomag_file1, machine='cryomag',
series='Pressure_0.0_GPa')
M = sample.add_measurement(mtype='thellier', mfile=cryomag_file2, machine='cryomag',
series='Pressure_1.0_GPa')
M = sample.add_measurement(mtype='thellier', mfile=cryomag_file3, machine='cryomag',
series='Pressure_0.0_GPa')
RockPy.save(sample, 'TTtest.rpy', RockPy.test_data_path)
else:
sample = RockPy.load('TTtest.rpy', RockPy.test_data_path)
return sample
def get_hys_all_sample():
folder = RockPy.test_data_path
S = RockPy.Sample(name='test_sample',
mass=14.2,
mass_unit='mg',
diameter=5.4,
length_unit='nm',
height=23.8)
mfile1 = join(folder, 'MUCVSM_test.hys')
mfile2 = join(folder, 'MUCVFTB_test.hys')
S.add_measurement(mtype='hys', mfile=mfile1, machine='vsm')
S.add_measurement(mtype='hys', mfile=mfile2, machine='vftb')
return S
def test():
# thellier output file from cryomag
cryomag_file = 'test_data/NLCRY_Thellier_test.TT'
# creating a sample
sample = RockPy.Sample(name='1a', mass='1.0', mass_unit='mg')
# adding the measurement to the sample
M = sample.add_measurement(mtype='thellier',
mfile=cryomag_file,
machine='cryomag')
S = Arai(sample)
print S
S.show()
def _check_samplegroup_list(self, samplegroup):
"""
Checks if samplegroup is a list of samples, a list of sample_groups, a single sample or a single samplegroup
and converts them to be a list of samplegroups
:param samplegroup:
:return:
"""
# check for list
if isinstance(samplegroup, list):
# check for sample_group
if all(isinstance(item, RockPy.Sample)
for item in samplegroup): # all input == samples
samplegroup = [RockPy.SampleGroup(sample_list=samplegroup)]
elif all(
isinstance(item, RockPy.SampleGroup)
for item in samplegroup): # all input == sample_groups
samplegroup = samplegroup
elif all(isinstance(item, RockPy.Study)
for item in samplegroup): # all input == samples
sgs = []
for study in samplegroup:
sgs.extend(study.samplegroups)
samplegroup = sgs
else:
log.error(
'MIXED lists not allowed or no Sample/SampleGroup instance found'
)
return None
if isinstance(samplegroup, RockPy.Sample):
samplegroup = [RockPy.SampleGroup(sample_list=samplegroup)]
if isinstance(samplegroup, RockPy.SampleGroup):
samplegroup = [samplegroup]
if isinstance(samplegroup, RockPy.Study):
samplegroup = [samplegroup.all_samplegroup]
return samplegroup
def create_dummy_measurement(mtype,
mfile=None,
machine=None,
idx=0,
mdata=None,
sample=None):
s = RockPy.Sample(name='dummy_sample')
m = s.add_measurement(
mtype=mtype,
mfile=mfile,
machine=machine, # general
idx=idx,
mdata=mdata,
)
if sample:
m.sample_obj = sample
return m
def test_info_dict(self):
s = RockPy.Tutorials.sample.get_sample_with_multiple_hys()
sg = RockPy.SampleGroup(sample_list=[s, s])
s_keys, sg_keys = [], []
for mtype in s.info_dict['mtype_stype_sval'].keys():
for stype in s.info_dict['mtype_stype_sval'][mtype].keys():
for sval in s.info_dict['mtype_stype_sval'][mtype][stype].keys():
s_keys.append('_'.join([mtype, stype, str(sval)]))
for mtype in sg.info_dict['mtype_stype_sval'].keys():
for stype in sg.info_dict['mtype_stype_sval'][mtype].keys():
for sval in sg.info_dict['mtype_stype_sval'][mtype][stype].keys():
sg_keys.append('_'.join([mtype, stype, str(sval)]))
self.assertEqual(sorted(s_keys), sorted(sg_keys))
def test():
# SG = get_thellier_samplegroup()
# SG = get_hys_coe_irm_rmp_sample_group()
S = RockPy.load('hys_coe_irm_rmp.rpy', '/Users/mike/Desktop/')