def generate_import_info(self, mtype=None, fpath=None, ftype=None, idx=None, series=None):
"""
First generate the file info. It is read from the fname, if possible.
After that the mtype, ftype, fpath and idx will be overwritten, assuming that you gave a proper
filname.
"""
out = {'mtype': mtype, 'fpath': fpath, 'ftype': ftype, 'idx': idx, 'series': series}
file_info = dict()
with RockPy3.ignored(ValueError):
file_info = RockPy3.core.file_operations.get_info_from_fname(path=fpath)
if not file_info:
self.log.warning(
'CANNOT readin fpath automatically.',
extra='See RockPy naming conventions for proper naming scheme.')
fname = RockPy3.get_fname_from_info(samplegroup='SG', sample_name=self.name, mtype=mtype, ftype=ftype,
series=series)
self.log.info('FILE NAME proposition:')
self.log.info('-'.join('' for i in range(50)))
self.log.info('%s' % fname)
self.log.info('-'.join('' for i in range(50)))
self.log.info('Please check for consistency and add samplegroup and mass, height, diameter')
else:
for check in ['mtype', 'ftype', 'series']:
if check in file_info and locals()[check]:
if not out[check] == file_info[check]:
self.log.warning(
'!!! INPUT != file_name: info does not match. Please check input, assuming filename correct')
self.log.warning('!!! {} != {}'.format(locals()[check], file_info[check]))
out.update(file_info)
out.pop('name', None)
return out
def plot(self, gname=None,
sname=None,
mtype=None,
series=None,
stype=None, sval=None, sval_range=None,
mean=False, groupmean=False,
invert=False,
id=None, **plt_props):
samples = self.get_sample(sname=sname,
mtype=mtype,
series=series,
stype=stype, sval=sval, sval_range=sval_range,
mean=mean,
invert=invert,
)
mlists = [[m for m in s.get_measurement(mtype=mtype, series=series,
stype=stype, sval=sval, sval_range=sval_range,
mean=mean, invert=invert, id=id) if m._visuals] for s in samples]
columns = max(len(ml) for ml in mlists)
if any(m for m in mlists):
fig = RockPy3.Figure(title=self.name, columns=columns)
for ml in mlists:
for m in ml:
vidx = deepcopy(fig._n_visuals)
m.add_visuals(fig, **plt_props)
v = fig.visuals[vidx][2]
v.title = ' '.join((m.sobj.name, v.title))
if m.has_series():
stuples = '\n'.join('{}'.format(s) for s in m.series)
with RockPy3.ignored(IndexError):
fig.visuals[vidx][2].add_feature('generic_text', transform='ax', s=stuples, x=0.05, y=0.9)
fig.show()
def plot(self,
mtype=None,
series=None,
stype=None, sval=None, sval_range=None,
mean=False,
invert=False,
id=None,
result=None, **plt_props):
mlist = self.get_measurement(mtype=mtype,
series=series, stype=stype, sval=sval, sval_range=sval_range,
mean=mean, invert=invert, id=id, result=result)
# max_columns = max(len(m._visuals) for m in mlist)
max_columns = sum(len(m._visuals) for m in mlist) if len(mlist) < 4 else max(len(m._visuals) for m in mlist)
fig = RockPy3.Figure(title=self.name, columns=max_columns)
for m in mlist:
# get index of the first visual of this measurement
vidx = deepcopy(fig._n_visuals)
# only add the measurement if it has _visuals defined (e.g. no mass measurements)
if m._visuals:
m.add_visuals(fig, **plt_props)
if m.has_series():
stuples = '\n'.join('{}'.format(s) for s in m.series)
with RockPy3.ignored(IndexError):
fig.visuals[vidx][2].add_feature('generic_text', transform='ax', s=stuples, x=0.05, y=0.9)
fig.show()
def plot(self,
gname=None,
sname=None,
mtype=None,
series=None,
stype=None,
sval=None,
sval_range=None,
mean=False,
groupmean=False,
invert=False,
id=None,
**plt_props):
samples = self.get_sample(
sname=sname,
mtype=mtype,
series=series,
stype=stype,
sval=sval,
sval_range=sval_range,
mean=mean,
invert=invert,
)
mlists = [[
m for m in s.get_measurement(mtype=mtype,
series=series,
stype=stype,
sval=sval,
sval_range=sval_range,
mean=mean,
invert=invert,
id=id) if m._visuals
] for s in samples]
columns = max(len(ml) for ml in mlists)
if any(m for m in mlists):
fig = RockPy3.Figure(title=self.name, columns=columns)
for ml in mlists:
for m in ml:
vidx = deepcopy(fig._n_visuals)
m.add_visuals(fig, **plt_props)
v = fig.visuals[vidx][2]
v.title = ' '.join((m.sobj.name, v.title))
if m.has_series():
stuples = '\n'.join('{}'.format(s) for s in m.series)
with RockPy3.ignored(IndexError):
fig.visuals[vidx][2].add_feature('generic_text',
transform='ax',
s=stuples,
x=0.05,
y=0.9)
fig.show()
def generate_import_info(self,
mtype=None,
fpath=None,
ftype=None,
idx=None,
series=None):
"""
First generate the file info. It is read from the fname, if possible.
After that the mtype, ftype, fpath and idx will be overwritten, assuming that you gave a proper
filname.
"""
out = {
'mtype': mtype,
'fpath': fpath,
'ftype': ftype,
'idx': idx,
'series': series
}
file_info = dict()
with RockPy3.ignored(ValueError):
file_info = RockPy3.core.file_operations.get_info_from_fname(
path=fpath)
if not file_info:
self.log.warning(
'CANNOT readin fpath automatically.',
extra='See RockPy naming conventions for proper naming scheme.'
)
fname = RockPy3.get_fname_from_info(samplegroup='SG',
sample_name=self.name,
mtype=mtype,
ftype=ftype,
series=series)
self.log.info('FILE NAME proposition:')
self.log.info('-'.join('' for i in range(50)))
self.log.info('%s' % fname)
self.log.info('-'.join('' for i in range(50)))
self.log.info(
'Please check for consistency and add samplegroup and mass, height, diameter'
)
else:
for check in ['mtype', 'ftype', 'series']:
if check in file_info and locals()[check]:
if not out[check] == file_info[check]:
self.log.warning(
'!!! INPUT != file_name: info does not match. Please check input, assuming filename correct'
)
self.log.warning('!!! {} != {}'.format(
locals()[check], file_info[check]))
out.update(file_info)
out.pop('name', None)
return out
def convert2float_or_str(item):
"""
Converts an item to a float or if not possible returns the str
Parameters
----------
item: str
Returns
-------
str, float
"""
with RockPy3.ignored(ValueError):
item = float(item)
return item
def convert2float_or_str(item):
"""
Converts an item to a float or if not possible returns the str
Parameters
----------
item: str
Returns
-------
str, float
"""
with RockPy3.ignored(ValueError):
item = float(item)
return item
def plot(self,
mtype=None,
series=None,
stype=None,
sval=None,
sval_range=None,
mean=False,
invert=False,
id=None,
result=None,
**plt_props):
mlist = self.get_measurement(mtype=mtype,
series=series,
stype=stype,
sval=sval,
sval_range=sval_range,
mean=mean,
invert=invert,
id=id,
result=result)
# max_columns = max(len(m._visuals) for m in mlist)
max_columns = sum(len(m._visuals)
for m in mlist) if len(mlist) < 4 else max(
len(m._visuals) for m in mlist)
fig = RockPy3.Figure(title=self.name, columns=max_columns)
for m in mlist:
# get index of the first visual of this measurement
vidx = deepcopy(fig._n_visuals)
# only add the measurement if it has _visuals defined (e.g. no mass measurements)
if m._visuals:
m.add_visuals(fig, **plt_props)
if m.has_series():
stuples = '\n'.join('{}'.format(s) for s in m.series)
with RockPy3.ignored(IndexError):
fig.visuals[vidx][2].add_feature('generic_text',
transform='ax',
s=stuples,
x=0.05,
y=0.9)
fig.show()
def get_measurement_infos(self, raw_info_header):
"""
takes the raw data and creates a dictionary with the measurement infos
"""
def separate(line):
if line:
if any(j in line for j in ('+', '-', '\"')):
splitter = 30
else:
splitter = 31
if line[splitter + 1:].rstrip():
out = (line[:splitter].rstrip().lower(),
self.convert2float_or_str(line[splitter +
1:].strip()))
if out[1] == 'Yes':
return (line[:splitter].rstrip().lower(), True)
if out[1] == 'No':
return (line[:splitter].rstrip().lower(), False)
else:
return out
t = [i.split(' ') for i in raw_info_header]
t = [[j for j in i if j] for i in t]
t = [tuple(i) for i in t if len(i) > 1]
data = {i[0].lower(): i[1] for i in t}
for k, v in data.items():
with RockPy3.ignored(ValueError):
data[k] = float(v)
if v == 'Yes':
data[k] = True
if v == 'No':
data[k] = False
return dict(data)
def show(
self,
xlim=None,
ylim=None,
equal_lims=False,
center_lims=False,
save_path=None,
pad=0.4,
w_pad=0.5,
h_pad=1.0,
file_name=None,
format='pdf',
legend=True,
sort_labels=True,
return_figure=False,
append_to_filename='',
):
"""
calls all visuals
Raises
------
TypeError if no visuals have been added
"""
self._fig, self.axes = self._create_fig(xsize=self.xsize,
ysize=self.ysize)
if not self.visuals:
self.log.error(
'NO VISUALS ADDED! Please add any of the followig visuals:')
for visual in sorted(Visual.implemented_visuals()):
self.log.info('\t %s' % visual)
raise TypeError('add a visual')
# actual plotting of the visuals
self.plt_all()
for name, type, visual in self._visuals:
if visual.xlim:
visual.ax.set_xlim(visual.xlim)
if visual.ylim:
visual.ax.set_ylim(visual.ylim)
if visual.xscale:
visual.ax.set_xscale(visual.xscale)
if visual.yscale:
visual.ax.set_yscale(visual.yscale)
# prevent scientific notation for x axis
# if type in ('thermocurve', ):
visual.ax.ticklabel_format(style='plain', axis='x')
# else:
# xlim = visual.ax.get_xlim()
# ylim = visual.ax.get_ylim()
if xlim == 'equal' or ylim == 'equal' or equal_lims:
if equal_lims:
xlim, ylim = self.get_xylims()
if center_lims:
xl = max(np.abs(xlim))
yl = max(np.abs(ylim))
xlim = [-xl, xl]
ylim = [-yl, yl]
# cycle through visuals to set
for name, type, visual in self._visuals:
if xlim == 'equal' or equal_lims:
visual.ax.set_xlim(xlim)
if ylim == 'equal' or equal_lims:
visual.ax.set_ylim(ylim)
# prepare legends for individual visuals
for name, type, visual in self._visuals:
# check if the legend should be drawn accoring to the visual.legend dictionary
if not visual.show_legend():
continue
if not legend:
break
handles, labels = visual.ax.get_legend_handles_labels()
if not all(i for i in (handles, labels)):
continue
# sorting of labels
if sort_labels:
labels, handles = zip(
*sorted(zip(labels, handles), key=lambda t: t[0]))
visual.ax.legend(handles, labels, **visual.legend_options)
# check if two entries and each is float or int
if xlim:
if len(xlim) == 2 and any(
isinstance(i, (float, int)) for i in xlim):
for name, type, visual in self._visuals:
visual.ax.set_xlim(xlim)
# check if two entries and each is float or int
if ylim:
if len(ylim) == 2 and any(
isinstance(i, (float, int)) for i in ylim):
for name, type, visual in self._visuals:
visual.ax.set_ylim(ylim)
self._fig.set_tight_layout(tight={
'pad': pad,
'w_pad': w_pad,
'h_pad': h_pad
})
if self.title:
self._fig.suptitle(self.title, fontsize=20)
# (left, bottom, right, top) in the normalized figure coordinate that the whole subplots area
# (including labels) will fit into
self._fig.set_tight_layout(tight={'rect': (0, 0, 1, 0.95)})
if return_figure:
return self._fig
if save_path:
if save_path.lower() == 'desktop':
if not file_name:
file_name = os.path.basename(inspect.stack()[-1][1])
file_name += append_to_filename
save_path = os.path.join(os.path.expanduser('~'), 'Desktop',
file_name)
else:
save_path = os.path.join(save_path, file_name)
if not format in file_name:
save_path += '.'
save_path += format
plt.savefig(save_path)
else:
with RockPy3.ignored(AttributeError):
self._fig.canvas.manager.window.raise_()
plt.show()
plt.close('all')
def get_info_from_fname(path=None): # todo redundant
"""
extracts the file information out of the filename
Parameters
----------
path:
complete path, with folder/fname. Will be split into the two
Raises
------
KeyError if ftype or mtype not in RockPy3.mtype_ftype_abbreviations_inversed
"""
# change add_measurement accordingly
folder = os.path.split(path)[0]
fname = os.path.split(path)[1]
fpath = fname
index = fname.split('.')[-1]
fname = fname.split('.')[:-1][0]
rest = fname.split('#')
samplegroup, sample_name, mtype, ftype = rest[0].split('_')
sample_info = [i.strip(']').split('[') for i in rest[1].split('_')]
mass, diameter, height = sample_info
if rest[2]:
series = rest[2]
# separate the series (combined with ;)
series = series.split(';')
# change , -> .
series = [i.replace(',', '.').split('_') for i in series]
series = [(i[0], float(i[1]), i[2]) for i in series]
else:
series = None
try:
STD = [int(i.lower().strip('std')) for i in rest if 'std' in i.lower()][0]
except IndexError:
STD = None
try:
options = [i.split('_') for i in rest[4].split('.')[0].split(';')]
options = {i[0]: i[1] for i in options}
except IndexError:
options = None
# convert mass to float
with RockPy3.ignored(ValueError):
mass[0] = mass[0].replace(',', '.')
mass[0] = float(mass[0])
# convert height to float
with RockPy3.ignored(ValueError):
diameter[0] = diameter[0].replace(',', '.')
diameter[0] = float(diameter[0])
# convert diameter to float
with RockPy3.ignored(ValueError):
height[0] = height[0].replace(',', '.')
height[0] = float(height[0])
if diameter[1] and height[1]:
if diameter[1] != height[1]:
diameter[0] = diameter[0] * getattr(ureg, height[1]).to(
getattr(ureg, diameter[1])).magnitude
mtype = mtype.lower() # convert to upper for ease of checking
ftype = ftype.lower() # convert to upper for ease of checking
try:
mtype = RockPy3.mtype_ftype_abbreviations_inversed[mtype]
except KeyError:
raise KeyError('%s not implemented yet' % mtype)
return
try:
ftype = RockPy3.mtype_ftype_abbreviations_inversed[ftype]
except KeyError:
raise KeyError('%s not implemented yet' % mtype)
return
# replace 'xml' ending with idx:
if index == 'xml':
index = 1
out = {
'samplegroup': samplegroup,
'sample_name': sample_name, # not needed since 3.5 rewrite
'mtype': mtype,
'ftype': ftype,
'fpath': join(folder, fpath),
'series': series,
# 'std': STD,
'idx': int(index),
'mass': None,
'mass_unit': None,
'diameter': None,
'height': None,
'length_unit': None,
}
# if mtype == 'mass':
if mass[0]:
out.update({'mass': mass[0],
'mass_unit': mass[1]})
# if mtype == 'diameter':
if diameter[0]:
out.update({'diameter': diameter[0],
'length_unit': diameter[1]})
# if mtype == 'height':
if height[0]:
out.update({'height': height[0],
'length_unit': diameter[1]})
if options:
out.update(options)
return out
def get_info_from_fname(path=None): # todo redundant
"""
extracts the file information out of the filename
Parameters
----------
path:
complete path, with folder/fname. Will be split into the two
Raises
------
KeyError if ftype or mtype not in RockPy3.mtype_ftype_abbreviations_inversed
"""
# change add_measurement accordingly
folder = os.path.split(path)[0]
fname = os.path.split(path)[1]
fpath = fname
index = fname.split('.')[-1]
fname = fname.split('.')[:-1][0]
rest = fname.split('#')
samplegroup, sample_name, mtype, ftype = rest[0].split('_')
sample_info = [i.strip(']').split('[') for i in rest[1].split('_')]
mass, diameter, height = sample_info
if rest[2]:
series = rest[2]
# separate the series (combined with ;)
series = series.split(';')
# change , -> .
series = [i.replace(',', '.').split('_') for i in series]
series = [(i[0], float(i[1]), i[2]) for i in series]
else:
series = None
try:
STD = [
int(i.lower().strip('std')) for i in rest if 'std' in i.lower()
][0]
except IndexError:
STD = None
try:
options = [i.split('_') for i in rest[4].split('.')[0].split(';')]
options = {i[0]: i[1] for i in options}
except IndexError:
options = None
# convert mass to float
with RockPy3.ignored(ValueError):
mass[0] = mass[0].replace(',', '.')
mass[0] = float(mass[0])
# convert height to float
with RockPy3.ignored(ValueError):
diameter[0] = diameter[0].replace(',', '.')
diameter[0] = float(diameter[0])
# convert diameter to float
with RockPy3.ignored(ValueError):
height[0] = height[0].replace(',', '.')
height[0] = float(height[0])
if diameter[1] and height[1]:
if diameter[1] != height[1]:
diameter[0] = diameter[0] * getattr(ureg, height[1]).to(
getattr(ureg, diameter[1])).magnitude
mtype = mtype.lower() # convert to upper for ease of checking
ftype = ftype.lower() # convert to upper for ease of checking
try:
mtype = RockPy3.mtype_ftype_abbreviations_inversed[mtype]
except KeyError:
raise KeyError('%s not implemented yet' % mtype)
return
try:
ftype = RockPy3.mtype_ftype_abbreviations_inversed[ftype]
except KeyError:
raise KeyError('%s not implemented yet' % mtype)
return
# replace 'xml' ending with idx:
if index == 'xml':
index = 1
out = {
'samplegroup': samplegroup,
'sample_name': sample_name, # not needed since 3.5 rewrite
'mtype': mtype,
'ftype': ftype,
'fpath': join(folder, fpath),
'series': series,
# 'std': STD,
'idx': int(index),
'mass': None,
'mass_unit': None,
'diameter': None,
'height': None,
'length_unit': None,
}
# if mtype == 'mass':
if mass[0]:
out.update({'mass': mass[0], 'mass_unit': mass[1]})
# if mtype == 'diameter':
if diameter[0]:
out.update({'diameter': diameter[0], 'length_unit': diameter[1]})
# if mtype == 'height':
if height[0]:
out.update({'height': height[0], 'length_unit': diameter[1]})
if options:
out.update(options)
return out
def show(self,
xlim=None, ylim=None,
equal_lims=False, center_lims=False,
save_path=None,
pad=0.4, w_pad=0.5, h_pad=1.0,
file_name=None, format='pdf',
legend=True, sort_labels = True,
return_figure=False,
append_to_filename = '',
):
"""
calls all visuals
Raises
------
TypeError if no visuals have been added
"""
self._fig, self.axes = self._create_fig(xsize=self.xsize, ysize=self.ysize)
if not self.visuals:
self.log.error('NO VISUALS ADDED! Please add any of the followig visuals:')
for visual in sorted(Visual.implemented_visuals()):
self.log.info('\t %s' % visual)
raise TypeError('add a visual')
# actual plotting of the visuals
self.plt_all()
for name, type, visual in self._visuals:
if visual.xlim:
visual.ax.set_xlim(visual.xlim)
if visual.ylim:
visual.ax.set_ylim(visual.ylim)
if visual.xscale:
visual.ax.set_xscale(visual.xscale)
if visual.yscale:
visual.ax.set_yscale(visual.yscale)
# prevent scientific notation for x axis
# if type in ('thermocurve', ):
visual.ax.ticklabel_format(style='plain', axis='x')
# else:
# xlim = visual.ax.get_xlim()
# ylim = visual.ax.get_ylim()
if xlim == 'equal' or ylim == 'equal' or equal_lims:
if equal_lims:
xlim, ylim = self.get_xylims()
if center_lims:
xl = max(np.abs(xlim))
yl = max(np.abs(ylim))
xlim = [-xl, xl]
ylim = [-yl, yl]
# cycle through visuals to set
for name, type, visual in self._visuals:
if xlim == 'equal' or equal_lims:
visual.ax.set_xlim(xlim)
if ylim == 'equal' or equal_lims:
visual.ax.set_ylim(ylim)
# prepare legends for individual visuals
for name, type, visual in self._visuals:
# check if the legend should be drawn accoring to the visual.legend dictionary
if not visual.show_legend():
continue
if not legend:
break
handles, labels = visual.ax.get_legend_handles_labels()
if not all(i for i in (handles, labels)):
continue
# sorting of labels
if sort_labels:
labels, handles = zip(*sorted(zip(labels, handles), key=lambda t: t[0]))
visual.ax.legend(handles, labels, **visual.legend_options)
# check if two entries and each is float or int
if xlim:
if len(xlim) == 2 and any(isinstance(i, (float, int)) for i in xlim):
for name, type, visual in self._visuals:
visual.ax.set_xlim(xlim)
# check if two entries and each is float or int
if ylim:
if len(ylim) == 2 and any(isinstance(i, (float, int)) for i in ylim):
for name, type, visual in self._visuals:
visual.ax.set_ylim(ylim)
self._fig.set_tight_layout(tight={'pad': pad, 'w_pad': w_pad, 'h_pad': h_pad})
if self.title:
self._fig.suptitle(self.title, fontsize=20)
# (left, bottom, right, top) in the normalized figure coordinate that the whole subplots area
# (including labels) will fit into
self._fig.set_tight_layout(tight={'rect': (0, 0, 1, 0.95)})
if return_figure:
return self._fig
if save_path:
if save_path.lower() == 'desktop':
if not file_name:
file_name = os.path.basename(inspect.stack()[-1][1])
file_name += append_to_filename
save_path = os.path.join(os.path.expanduser('~'), 'Desktop', file_name)
else:
save_path = os.path.join(save_path, file_name)
if not format in file_name:
save_path +='.'
save_path += format
plt.savefig(save_path)
else:
with RockPy3.ignored(AttributeError):
self._fig.canvas.manager.window.raise_()
plt.show()
plt.close('all')
