def showRegions(self, visibility, item):
isregion, par = self.isRegion(item)
if isregion:
par.opts['expanded'] = visibility
if not self.isInitializing:
try:
self.parent.plotwidget.draw_regions()
except Exception as e:
scp.error_(e)
def addDataset(self, dataset=None):
scp.debug_('Add a dataset')
# Read the dataset
try:
if not dataset:
dataset = scp.read(Qt_parent=self.parent, default_filter='omnic')
if dataset is None: # still not determined.
return
except Exception as e:
scp.error_(e)
# Create a subproject with this dataset
subproj = scp.Project()
self.project.add_project(subproj, dataset.name)
subproj.add_dataset(dataset, f'{dataset.name}/original')
# Signal
self.dirty = True
self.sigProjectChanged.emit('dataset added')
def _loadProject(self, *args, **kwargs):
"""
Load a project.
"""
if len(args)<1:
return
fname = args[0]
proj = None
if fname is None or fname in ['', 'untitled']:
# create a void project
proj = scp.Project(name='untitled')
else:
try:
proj = scp.Project.load(fname, **kwargs)
proj.meta['project_file'] = fname
except Exception as e:
scp.error_(e)
self.closeProject()
return proj
nd = NDDataset()
# %% [markdown]
# If something goes wrong with during a cell execution, a ``traceback`` is displayed.
#
# For instance, the object or method ``toto`` does not exist in the API, so an error (**ImportError**) is generated
# when trying to import this from the API.
#
# Here we catch the error with a conventional `try-except` structure
# %%
try:
from spectrochempy import toto
except ImportError as e:
scp.error_("OOPS, THAT'S AN IMPORT ERROR! : %s" % e)
# %% [markdown]
# The error will stop the execution if not catched.
#
# This is a basic behavior of python : on way to avoid. stoppping the execution without displaying a message is :
# %%
try:
from spectrochempy import toto # noqa: F811, F401
except Exception:
pass
# %% [markdown]
# ## API Configuration
#
d3D
# %% [markdown]
# Programmatically, we can use the attribute `is_empty` or `has_data` to check this
# %%
d3D.v.has_data, d3D.v.is_empty
# %% [markdown]
# An error is raised when a coordinate doesn't exist
# %%
try:
d3D.x
except KeyError as e:
scp.error_(e)
# %% [markdown]
# In some case it can also be useful to get a coordinate from its title instead of its name (the limitation is that if
# several coordinates have the same title, then only the first ones that is found in the coordinate list, will be
# returned - this can be ambiguous)
# %%
d3D["time"]
# %%
d3D.time
# %% [markdown]
# ## Labels
colormap='viridis',
nrow=2,
ncol=2,
sharex=True,
sharey=True,
dpi=100)
# %% [markdown]
# The four datasets `nd1` to `nd4` have some overlapping in both dimensions. But it we want for example to add `nd2`
# with `nd4`. This will fail because the dimension are not aligned.
# %%
try:
nd2 + nd4
except Exception as e:
scp.error_(str(e) + ' Cannot add unaligned datasets.')
# %% [markdown]
# Let try to align them, in the `y` dimension (*i.e.* the first) as this the one which differ in size.
# (NOTE: to find the actual names of the dimensions, just get the `dims` attribute of the datasets.
# %%
nd2.dims, nd4.dims
# %% [markdown]
# To align we can use different methods, depending on the expected results (missing values in the aligned datasets
# will be masked)
# %%
# `outer` method => union of the coordinates
nd2a, nd4a = scp.align(nd2, nd4, dim='y', method='outer')
# ##### exp
# Exponential of all elements in the input array, element-wise
# %%
out = np.exp(dataset)
_ = out.plot(figsize=(6, 2.5))
# %% [markdown]
# Obviously numpy exponential functions applies only to dimensionless array. Else an error is generated.
# %%
x = scp.NDDataset(np.arange(5), units="m")
try:
np.exp(x) # A dimensionality error will be generated
except DimensionalityError as e:
error_(e)
# %% [markdown]
# ##### exp2
# Calculate 2\*\*p for all p in the input array.
# %%
out = np.exp2(dataset)
_ = out.plot(figsize=(6, 2.5))
# %% [markdown]
# ##### expm1
# Calculate `exp(x) - 1` for all elements in the array.
# %%
out = np.expm1(dataset)
max_relative_error = max(error[nonzero] / abs(y.data[nonzero]))
return max(error), max_relative_error
# %%
max_error, max_rel_error = difference(S0, newS0)
print(f"Max absolute difference in absorbance: {max_error:.3g}")
print(f"Max relative difference in absorbance: {max_rel_error:.3g}")
# %%
max_error, max_rel_error = difference(S0.x, newS0.x)
print(f"Max absolute difference in wavenumber: {max_error:.3g}")
print(f"Max relative difference in wavenumber: {max_rel_error:.3g}")
# %% [markdown]
# This is much beyond the experimental accuracy but can lead to undesirable effects.
#
# For instance:
# %%
try:
S0 - newS0
except Exception as e:
scp.error_(e)
# %% [markdown]
# returns an error because of the small shift of coordinates. We will see in another tutorial how to re-align datasets
# and deal with these small problems. It is worth noticing that similar distortions arise in commercial software,...
# except that the user is not notified.
#
def test_logger(caplog):
logger = logging.getLogger('SpectroChemPy')
logger.propagate = True
caplog.set_level(logging.DEBUG)
# We can set the level using strings
set_loglevel("DEBUG")
assert logger.level == logging.DEBUG
set_loglevel(WARNING)
assert logger.level == logging.WARNING
error_('\n' + '*' * 80 + '\n')
debug_('debug in WARNING level - should not appear')
info_('info in WARNING level - should not appear')
warning_('OK this is a Warning')
error_('OK This is an Error')
error_('\n' + '*' * 80 + '\n')
set_loglevel(INFO)
assert logger.level == logging.INFO
debug_('debug in INFO level - should not appear')
info_('OK - info in INFO level')
warning_('OK this is a Warning')
error_('OK This is an Error')
error_('\n' + '*' * 80 + '\n')
set_loglevel('DEBUG')
assert logger.level == logging.DEBUG
debug_('OK - debug in DEBUG level')
info_('OK - info in DEBUG level')
assert caplog.records[-1].levelname == 'INFO'
assert caplog.records[-1].message == 'OK - info in DEBUG level'
warning_('OK this is a Warning')
assert caplog.records[-1].levelname == 'WARNING'
assert caplog.records[-1].message == 'OK this is a Warning'
error_('OK This is an Error')
assert caplog.records[-1].levelname == 'ERROR'
assert caplog.records[-1].message == 'OK This is an Error'
np.sqrt(x)
# %%
x = 10 * ur.radians
np.sin(x)
# %% [markdown]
# Consistency of the units are checked and errors are generated if quantities have not appropriate units
# with the math operation...
# %%
x = 10 * ur.meters
try:
np.cos(x)
except scp.DimensionalityError as e: # catch the error
scp.error_(e) # generate the error message (see API configuration)
# Consistency of the units are checked and errors are generated if quantities have not appropriate units
# with the math operation...
# %% [markdown]
# ## Stripping the units
#
# If for any reason - including quick and dirty checks -
# unitless numbers are needed, the `magnitude` field can be used:
# %%
x = 10 * ur.meters
np.cos(x.magnitude)
# %% [markdown]
nrow=2,
ncol=2,
sharex=True,
sharey=True,
dpi=100,
)
# %% [markdown]
# The four datasets `nd1` to `nd4` have some overlapping in both dimensions. But if we want for example to add `nd2`
# with `nd4`. This will fail because the dimension are not aligned.
# %%
try:
nd2 + nd4
except Exception as e:
scp.error_(str(e) + " Cannot add unaligned datasets.")
# %% [markdown]
# Let try to align them, in the `y` dimension (*i.e.* the first) as this the one which differ in size.
# (NOTE: to find the actual names of the dimensions, just get the `dims` attribute of the datasets).
# %%
nd2.dims, nd4.dims
# %% [markdown]
# To align we can use different methods, depending on the expected results (missing values in the aligned datasets
# will be masked)
# %%
# `outer` method => union of the coordinates
nd2a, nd4a = scp.align(nd2, nd4, dim="y", method="outer")
def test_logger(caplog):
logger = logging.getLogger("SpectroChemPy")
logger.propagate = True
caplog.set_level(DEBUG)
# We can set the level using strings
set_loglevel("DEBUG")
assert logger.handlers[0].level == INFO # DEBUG only on the file
assert logger.handlers[1].level == DEBUG
set_loglevel(WARNING)
assert logger.handlers[0].level == WARNING
assert logger.handlers[1].level == WARNING
error_("\n" + "*" * 80 + "\n")
debug_("debug in WARNING level - should not appear")
info_("info in WARNING level - should not appear")
warning_("OK this is a Warning")
error_("OK This is an Error")
error_("\n" + "*" * 80 + "\n")
set_loglevel(INFO)
assert logger.handlers[0].level == INFO
assert logger.handlers[1].level == INFO
debug_("debug in INFO level - should not appear on stdout")
info_("OK - info in INFO level")
warning_("OK this is a Warning")
error_("OK This is an Error")
error_("\n" + "*" * 80 + "\n")
set_loglevel("DEBUG")
assert logger.handlers[0].level == INFO
assert logger.handlers[1].level == DEBUG
debug_("OK - debug in DEBUG level")
info_("OK - info in DEBUG level")
assert caplog.records[-1].levelname == "INFO"
assert caplog.records[-1].message.endswith("OK - info in DEBUG level")
warning_("OK this is a Warning")
assert caplog.records[-1].levelname == "WARNING"
assert caplog.records[-1].message.endswith("OK this is a Warning")
error_("OK This is an Error")
assert caplog.records[-1].levelname == "ERROR"
assert caplog.records[-1].message.endswith("OK This is an Error")