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✨ Shift irf derivatives in plot_coherent_artifact by irf position #136

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Feb 3, 2023
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✨ Shift irf derivatives in plot_coherent_artifact by irf position #136

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17 changes: 12 additions & 5 deletions pyglotaran_extras/plotting/plot_coherent_artifact.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@
from pyglotaran_extras.io.load_data import load_data
from pyglotaran_extras.plotting.utils import abs_max
from pyglotaran_extras.plotting.utils import add_cycler_if_not_none
from pyglotaran_extras.plotting.utils import extract_irf_location
from pyglotaran_extras.plotting.utils import shift_time_axis_by_irf_location

if TYPE_CHECKING:
from cycler import Cycler
Expand All @@ -25,6 +27,7 @@ def plot_coherent_artifact(
*,
time_range: tuple[float, float] | None = None,
spectral: float = 0,
main_irf_nr: int | None = 0,
normalize: bool = True,
figsize: tuple[int, int] = (18, 7),
show_zero_line: bool = True,
Expand All @@ -47,6 +50,10 @@ def plot_coherent_artifact(
plot this value does not need to be an exact existing value and only has effect if the
IRF has dispersion. Defaults to 0 which means that the IRF derivative plot at lowest
spectral value will be shown.
main_irf_nr: int | None
Index of the main ``irf`` component when using an ``irf`` parametrized with multiple peaks
and is used to shift the time axis. If it is none ``None`` the shifting will be
deactivated. Defaults to 0.
normalize: bool
Whether or not to normalize the IRF derivative plot. If the IRF derivative is normalized,
the IRFAS is scaled with the reciprocal of the normalization to compensate for this.
Expand Down Expand Up @@ -80,7 +87,10 @@ def plot_coherent_artifact(
)
return fig, axes

irf_max = abs_max(dataset.coherent_artifact_response, result_dims=("coherent_artifact_order"))
irf_location = extract_irf_location(dataset, spectral, main_irf_nr)
irf_data = shift_time_axis_by_irf_location(dataset.coherent_artifact_response, irf_location)

irf_max = abs_max(irf_data, result_dims=("coherent_artifact_order"))
irfas_max = abs_max(
dataset.coherent_artifact_associated_spectra, result_dims=("coherent_artifact_order")
)
Expand All @@ -94,10 +104,7 @@ def plot_coherent_artifact(
irf_y_label = f"normalized {irf_y_label}"

plot_slice_irf = (
dataset.coherent_artifact_response.sel(spectral=spectral, method="nearest")
/ irf_max
* scales
/ norm_factor
irf_data.sel(spectral=spectral, method="nearest") / irf_max * scales / norm_factor
)
irf_sel_kwargs = (
{"time": slice(time_range[0], time_range[1])} if time_range is not None else {}
Expand Down