GUIs

These GUIs are part of the API package in order to bring some functionality to the user when working on the command line. Here, we solely use matloplib and Qt frontends. This is not the description of the main GUI, which can be found in Graphical User Interface.

Mass Calibration GUIs

Define the mass calibration by clicking on a plot.

`CreateMassCalibration`

class rimseval.guis.mcal.CreateMassCalibration(crd: CRDFileProcessor, logy=True, mcal: array = None, theme=None)

QMainWindow to create a mass calibration.

append_to_mcal(tof: float, mass: float) → None

Append a given value to the mass calibration.

Parameters:

tof – Time of flight.
mass – Mass.

apply(): Apply the mass calibration and return it.

check_mcal_length(): Check length of mcal to set button statuses, start guessing.

guess_mass(tof: float) → str

Guess the mass depending on what is currently set.

If not drawn from iniabu, I assume the user wants even masses!

Parameters:: tof – Time of Flight (us)
Returns:: Guessed mass.

query_mass(tof: float) → float | None

Query mass from user.

Query a mass from the user using a QInputDialog.

Parameters:: tof – Time of flight of the clicked area.
Returns:: Mass of the peak as given by user.

right_click_event(xpos: float, *args, **kwargs) → None: Act on an emitted right click event.

secondary_axis(params: List = None, visible: bool = False) → None

Toggle secondary axis.

Parameters:

params – Parameters for the transfer functions t0 and const. Only required when visible=True.
visible – Turn it on? If so, params are required.

signal_calibration_applied

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

undo_last_mcal(): Undo the last mass calibration by popping the last entry of list.

`create_mass_cal_app()`

rimseval.guis.mcal.create_mass_cal_app(crd: CRDFileProcessor, logy: bool = True, theme=None) → None

Create a PyQt5 app for the mass cal window.

Parameters:

crd – CRD file to calibrate for.
logy – Should the y axis be logarithmic? Defaults to True.
theme – Theme of GUI, requires pyqtdarktheme to be installed

`find_closest_iso()`

rimseval.guis.mcal.find_closest_iso(mass: float, key: List = None) → Tuple[str, float]

Find closest iniabu isotope to given mass and return its name.

If a key is given, will only consider that element, otherwise all.

Parameters:

mass – Mass of the isotope to look for.
key – An element or isotope key that is valid for iniabu.

Returns:

Closest isotpoe, name and mass as tuple.

Integrals & Background

Classes to define integrals and backgrounds. These are both very similar in nature, therefore, one superclass is created and individual routines subclass this one further.

`DefineAnyTemplate`

class rimseval.guis.integrals.DefineAnyTemplate(crd: CRDFileProcessor, logy=True, theme: str = None)

Template to define integrals and backgrounds.

apply(): Apply the mass calibration and return it.

button_pressed(name: str)

Define action for left click of a peak button.

Parameters:: name – Name of the peak.

check_peak_overlapping(peak_pos: array) → List | None

Check if a given peak position overlaps with any other peaks.

Parameters:: peak_pos – Position of peak, 2 entry array with from, to.
Returns:: List of all peak names that it overlaps or None.

clear_layout(layout) → None: Clear a given layout of all widgets, etc.

create_buttons(): Create the buttons in the right menubar.

mouse_right_press(xpos: float) → None

Act on right mouse button pressed.

Parameters:: xpos – Position on x axis.

mouse_right_released(xpos: float) → None

Right mouse button was released.

Parameters:: xpos – Position on x axis.

peaks_changed(): Go through the list of peaks, make buttons and shade areas.

shade_peaks(): Shade the peaks with given integrals.

sort_integrals(): Sort the names and integrals using routine from processor_utilities.

user_input(peak_pos: array, name: str = '') → None

Query user for position.

Parameters:

peak_pos – Sorted array, left and right position of peak.
name – Name to preset the line-edit with.

`DefineBackgrounds`

class rimseval.guis.integrals.DefineBackgrounds(crd: CRDFileProcessor, logy=True, theme: str = None)

QMainWindow to define backgrounds.

apply(): Apply the mass calibration and return it.

button_pressed(name: str)

Delete a peak from consideration names and values list.

Parameters:: name – Name of the peak.

peaks_changed(): Go through the list of peaks, make buttons and shade areas.

shade_backgrounds(): Go through background list and shade them.

Note

Canvas is not cleared prior to this!

signal_backgrounds_defined

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

user_input(bg_pos: array, name: str = '') → None

Query user for position of background.

Parameters:

bg_pos – Sorted array, left and right position of background.
name – Name of the peak, for reloading the UI.

`DefineIntegrals`

class rimseval.guis.integrals.DefineIntegrals(crd: CRDFileProcessor, logy=True, theme: str = None)

QMainWindow to define integrals.

apply(): Apply the mass calibration and return it.

button_pressed(name: str)

Delete a peak from consideration names and values list.

Parameters:: name – Name of the peak.

peaks_changed(): Go through the list of peaks, make buttons and shade areas.

signal_integrals_defined

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

user_input(peak_pos: array, name: str = '') → None

Query user for position.

Parameters:

peak_pos – Sorted array, left and right position of peak.
name – Name to pre-populate line-edit with.

`define_backgrounds_app()`

rimseval.guis.integrals.define_backgrounds_app(crd: CRDFileProcessor, logy: bool = True) → None

Create a PyQt5 app for defining backgruonds.

Parameters:

crd – CRD file to calibrate for.
logy – Should the y axis be logarithmic? Defaults to True.

`define_integrals_app()`

rimseval.guis.integrals.define_integrals_app(crd: CRDFileProcessor, logy: bool = True) → None

Create a PyQt5 app for defining integrals.

Parameters:

crd – CRD file to calibrate for.
logy – Should the y axis be logarithmic? Defaults to True.

`tableau_color()`

rimseval.guis.integrals.tableau_color(it: int = 0) → str

Return nth color from matplotlib TABLEAU_COLORS.

If out of range, start at beginning.

Parameters:: it – Which tableau color to get.
Returns:: Matplotlib color string.

Matplotlib Canvas Classes

These classes create spectra plotters and handling for theses specific tasks. Uses the matplotlib Qt5Agg backend.

`PlotSpectrum`

Plots the spectrum and serves it as a matplotlib figure. It adds toolbar and canvas (see below) plus makes two layouts available, a bottom layout and a right layout. This allows the addition to QWidgets into this layouts later on.

The plot widget adds one button in the bottom layout to toggle logarithmic axes for the vertical / signal axis.

class rimseval.guis.mpl_canvas.PlotSpectrum(crd: CRDFileProcessor, logy: bool = True, theme: str = None)

QMainWindow to plot a ToF or mass spectrum.

logy_toggle(): Toggle logy.

plot_ms(): Plot mass spectrum.

plot_tof(): Plot ToF spectrum.

`MplCanvasRightClick`

Handle right-click on matplotlib canvas. Releases to signals: one on right mouse button press and one on right mouse button release. These signals send the x and y position where the mouse event took place.

class rimseval.guis.mpl_canvas.MplCanvasRightClick(figure: Figure)

MPL Canvas reimplementation to catch right click.

On right click, emits the coordinates of the position in axes coordinates as a signal of two floats (x_position, y_position).

emit_mouse_position(event, case)

Emit a signal on a right mouse click event.

Here, bring up a box to ask for the mass, then send it, along with the time the mass is at, to the parent class receiver.

Parameters:

event – PyQt event.
case – Which case are we handling? Currently implemented are “pressed”, “released”.

mouse_right_press_position

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

mouse_right_release_position

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

`MyMplNavigationToolbar`

Re-implementation of the matplotlib navigation toolbar. After zooming in, the zoom function is automatically deactivated.

class rimseval.guis.mpl_canvas.MyMplNavigationToolbar(*args, **kwargs)

My own reimplementation of the navigation toolbar.

Features: - untoggle zoom button after zoom is finished.

release_pan(event): Run a normal pan release event and then untoggle button.

release_zoom(event): Run a normal zoom release event and then untoggle button.

Plots

These routines allow for specialty plots, i.e., to plot figures that are enot regularly used or needed during data evaluation but can give useful further information on the instrument, etc.

`dt_ions()`

Create a PyQt app and run it.

rimseval.guis.plots.dt_ions(crd: CRDFileProcessor, logy: bool = False, theme: str = None, max_ns: float = None) → None

Plot ToF difference between ions for shots with 2+ ions.

Parameters:

crd – CRD file to process.
logy – Plot with logarithmic y axis? Defaults to True
theme – Theme to plot in, defaults to None.
max_ns – Maximum time to plot in ns. If None, plots all.

`integrals_packages()`

Create a PyQt app and run it.

rimseval.guis.plots.integrals_packages(crd: CRDFileProcessor, logy: bool = False, theme: str = None) → None

Plot all the integrals versus package number for data split into packages.

Parameters:

crd – CRD file to process.
logy – Plot with logarithmic y axis? Defaults to True
theme – Theme to plot in, defaults to None.

`nof_ions_per_shot()`

Create a PyQt app and run it.

rimseval.guis.plots.nof_ions_per_shot(crd: CRDFileProcessor, logy: bool = False, theme: str = None) → None

Plot a histogram of the number of shots in a given crd file.

The histogram is compared with the theoretical curve based on poisson statistics.

Parameters:

crd – CRD file to process.
logy – Plot with logarithmic y axis? Defaults to True
theme – Theme to plot in, defaults to None.

`PlotFigure`

Class to plot a figure.

class rimseval.guis.plots.PlotFigure(logy: bool = False, theme: str = None)

QMainWindow to plot a Figure.

logy_toggle(): Toggle logy.

`DtIons`

Matplotlib PyQt figure to plot histogram for arrival time differences between ions.

class rimseval.guis.plots.DtIons(crd: CRDFileProcessor, logy: bool = False, theme: str = None, max_ns: float = None)

Plot time differences between ions.

calc_and_draw() → None: Calculate the required data and draw it.

`IntegralsPerPackage`

Matplotlib PyQt figure to integrals per package.

class rimseval.guis.plots.IntegralsPerPackage(crd: CRDFileProcessor, logy: bool = False, theme: str = None)

Plot integrals of all packages versus package number.

calc_and_draw() → None: Create the plot for all the defined integrals.

`IonsPerShot`

Matplotlib PyQt figure to plot histogram of ions per shot.

class rimseval.guis.plots.IonsPerShot(crd: CRDFileProcessor, logy: bool = False, theme: str = None)

Plot histogram for number of ions per shot.

calc_and_draw() → None: Calculate the histogram and plot it.