def test_baselinecorrector_load_clicked(X, monkeypatch):
def open_ok(*args, **kwargs):
# mock opening a dialog
return SPG_FILE
def open_cancel(*args, **kwargs):
# mock dialog canceled
return None
def open_wrong(*args, **kwargs):
# mock opening a dialog
return UNREADABLE
out = scp.BaselineCorrector()
assert out.corrected.is_empty
# save
# write without parameters and dialog cancel
monkeypatch.setenv(
"KEEP_DIALOGS", "True"
) # we ask to display dialogs as we will mock them.
monkeypatch.setattr(spectrochempy.core, "open_dialog", open_cancel)
assert out._load_clicked() is None
monkeypatch.setattr(spectrochempy.core, "open_dialog", open_ok)
out._load_clicked()
assert out.original.name == "nh4y-activation"
out = scp.BaselineCorrector()
monkeypatch.setattr(spectrochempy.core, "open_dialog", open_wrong)
out._load_clicked()
assert out.original.is_empty
def test_baselinecorrector_save_clicked(X, monkeypatch):
def dialog_cancel(*args, **kwargs):
# mock a dialog cancel action
return None
def dialog_save(*args, **kwargs):
# mock a dialog to save
return "spec.scp"
out = scp.BaselineCorrector(X)
# save
# write without parameters and dialog cancel
monkeypatch.setenv(
"KEEP_DIALOGS", "True"
) # we ask to display dialogs as we will mock them.
monkeypatch.setattr(spectrochempy.core, "save_dialog", dialog_cancel)
assert out._save_clicked() is None
monkeypatch.setattr(spectrochempy.core, "save_dialog", dialog_save)
filename = out._save_clicked()
assert filename == scp.pathclean("spec.scp") # <-
assert filename.exists()
if filename.exists:
filename.unlink()
def test_baselinecorrector_parameters(X):
_X = X[0:10, 0:100]
out = scp.BaselineCorrector(_X)
# sequential
assert out._method_selector in out._method_control.children
assert out._npc_slider not in out._method_control.children
out._interpolation_selector.value = "pchip"
out._process_clicked()
# try higher polyorder
out._order_slider.value = 3
out._interpolation_selector.value = "polynomial"
out._process_clicked()
assert out.corrected.shape == (10, 100)
assert len(out._fig.axes[0].lines) == 20, "original + baselines"
assert len(out._fig.axes[1].lines) == 10, "corrected"
assert np.all(out._fig.axes[1].lines[0].get_xdata() == _X.x.data)
# try multivariate
out._method_selector.value = "multivariate"
assert out._method_selector in out._method_control.children
assert out._npc_slider in out._method_control.children
# try multivariate, with 2 pcs
out._npc_slider.value = 2
out._process_clicked()
out._method_selector.value = "sequential"
assert out._method_selector in out._method_control.children
assert out._npc_slider not in out._method_control.children
# datasets
# * `save as`: save the baseline corrected dataset.
#
# The `x slice` and `y slice` text boxes can be used to slice the original dataset
# with the usual `[start:stop:step]` format. In both dimensions, coordinates or indexes
# can be used (for example, [3000.0::2] or [:100:5] are valid entries).
#
# The `Method` and `Interpolation` dropdown fields are self-explanatory,
# see above for details.
#
# `Ranges` must be entered as a tuple of digits or wave numbers,
# e.g. `([5900.0, 5400.0], 2000.0, [1550.0, 1555.0],)`.
# %%
X = scp.read_omnic("irdata/nh4y-activation.spg")
out = scp.BaselineCorrector(X)
# %% [markdown]
# After processing, one can get the original (sliced) dataset, corrected dataset
# and baselines
# through the following attributes:
# %%
out.original, out.corrected, out.baseline
# %% [markdown]
# <div class='alert alert-info'>
# <b>Exercises</b>
#
# **basic:**
# - write commands to subtract (i) the first spectrum from a dataset and (ii)
def test_baselinecorrector_slicing(X):
out = scp.BaselineCorrector(X)
assert out.corrected.shape == (55, 5549)
assert len(out._fig.axes[0].lines) == 110, "original + baselines"
assert len(out._fig.axes[1].lines) == 55, "corrected"
assert np.all(out._fig.axes[1].lines[0].get_xdata() == X.x.data)
assert np.all(out._fig.axes[0].lines[10].get_ydata() == X.data[10])
# slicing
out._x_limits_control.value = "[5000.56 : 649.9 : 1]"
out._y_limits_control.value = "[0:55:2]"
out._process_clicked()
assert len(out._fig.axes[0].lines) == 56, "original + baselines"
assert len(out._fig.axes[1].lines) == 28, "corrected"
assert np.all(out._fig.axes[1].lines[0].get_xdata() == X.x[5000.56:649.9].data)
assert np.all(out._fig.axes[0].lines[1].get_ydata() == X[2, 5000.56:649.9].data)
out._x_limits_control.value = "[5400.56 : 800.9 : 1]"
out._ranges_control.value = """
(
[5900.0, 5400.0],
[4000.0, 4500.0],
4550.0,
[2100.0, 2000.0],
[1550.0, 1555.0],
[1250.0, 1300.0],
[800.0, 850.0],
)
"""
out._process_clicked()
assert out.corrected.shape == (28, 4771)
initial_ranges = (
[5900.0, 5400.0],
[4000.0, 4500.0],
4550.0,
[2100.0, 2000.0],
[1550.0, 1555.0],
[1250.0, 1300.0],
[800.0, 850.0],
)
out2 = scp.BaselineCorrector(X, initial_ranges=initial_ranges)
out2._x_limits_control.value = "[5400.56 : 800.9 : 1]"
out2._process_clicked()
assert np.all(out2._fig.axes[1].lines[0].get_xdata() == X.x[5400.56:800.9].data)
assert np.all(
out._fig.axes[1].lines[0].get_xdata() == out2._fig.axes[1].lines[0].get_xdata()
)
# slicing limits out of coord range
out = scp.BaselineCorrector(X[::50, :])
out._x_limits_control.value = "[4000.0 : 2000.0 : 1]"
out._ranges_control.value = """
(
[5900.0, 5400.0],
[800.0, 850.0],
)
"""
out._process_clicked()
assert out.corrected.shape == (2, 2075)
out._ranges_control.value = """
(
5900.,
[800.0, 850.0],
)
"""
out._process_clicked()
assert out.corrected.shape == (2, 2075)
out._ranges_control.value = """
(
[5900.0, 5400.0],
850.0
)
"""
out._process_clicked()
assert out.corrected.shape == (2, 2075)
# other slicing format
out = scp.BaselineCorrector(X)
out._y_limits_control.value = "[0.0:3000.0:1]" # y location
out._process_clicked()
assert out.corrected.shape == (6, 5549)
# missing parts in slice
out._y_limits_control.value = "[:3000.0]" # y location
out._process_clicked()
assert out.corrected.shape == (6, 5549)
out._y_limits_control.value = "::2" # y location
out._process_clicked()
assert out.corrected.shape == (28, 5549)
out._y_limits_control.value = "0:10:2" # y location
out._process_clicked()
assert out.corrected.shape == (5, 5549)
out._x_limits_control.value = "::100" # y location
out._process_clicked()
assert out.corrected.shape == (5, 56)
out._x_limits_control.value = "::100:" # y location
with pytest.raises(ValueError):
out._process_clicked()
def test_baselinecorrector_not_a_NDDataset(X):
with pytest.raises(ValueError):
scp.BaselineCorrector(X.x)