h5analysis.MathData.Object3dHistogramReduce

class h5analysis.MathData.Object3dHistogramReduce

Bases: Load1d

Apply transformations to a 3d image stack

Methods

add()

This method is not defined

apply_kwargs([norm, xoffset, xcoffset, ...])

Apply math to 1d reduced objects

background()

This method is not defined

export(filename[, split_files])

Export and write data to specified file.

exportWidgetStep()

Helper function for exporter widget.

exporter()

Interactive exporter widget.

get_data()

Make data available in memory as exported to file.

hline(pos, **kwargs)

Draw a horizontal line in the plot.

label(pos_x, pos_y, text, **kwargs)

Draw a text box in the plot.

load(obj, line, scan)

Loader for 3d object

loadObj()

This method is not defined

plot([linewidth, title, xlabel, ylabel, ...])

Plot all data assosciated with class instance/object.

plot_legend(pos)

Overwrite default legend position.

polygon(polygon[, exact])

Mask array defined by a polygon and sum over specified axis

save_plot(fname, **kwargs)

Create a matplotlib plot window

show_fluorescence(element, siegbahn_symbol)

Draw a line in the plot for the requested fluorescence line.

stitch()

This method is not defined

subtract()

This method is not defined

vline(pos, **kwargs)

Draw a vertical line in the plot.

xlim(lower, upper)

Set x-axis limits applied to data stream.

ylim(lower, upper)

Set y-axis limits applied to data stream.
add()

This method is not defined

apply_kwargs(norm=False, xoffset=None, xcoffset=None, yoffset=None, ycoffset=None, grid_x=[None, None, None], savgol=None, binsize=None)

Apply math to 1d reduced objects

Parameters:

  • norm (boolean) – normalizes to [0,1]

  • xoffset (list) – fitting offset (x-stream)

  • xcoffset (float) – constant offset (x-stream)

  • yoffset (list) – fitting offset (y-stream)

  • ycoffset (float) – constant offset (y-stream)

  • grid_x (list) – grid data evenly with [start,stop,delta]

  • savgol (tuple) – (window length, polynomial order, derivative)

  • binsize (int) – puts data in bins of specified size

background()

This method is not defined

export(filename, split_files=False)

Export and write data to specified file.

Parameters:

  • filename (string)

  • split_files (Boolean) – Sets whether scans are exported appended to one file (False), or separately (True)

exportWidgetStep()

Helper function for exporter widget.

exporter()

Interactive exporter widget.

get_data()

Make data available in memory as exported to file.

Returns:

  • dfT (pandas DataFrame) – All loaded data.

  • files (list) – List of all loaded files.

hline(pos, **kwargs)

Draw a horizontal line in the plot.

Parameters:

  • pos (float)

  • **kwargs (dict, optional) – See bokeh manual for available options.

label(pos_x, pos_y, text, **kwargs)

Draw a text box in the plot.

Parameters:

  • pos_x (float)

  • pos_y (float)

  • text (string)

  • **kwargs (dict, optional) – See bokeh manual for available options.

load(obj, line, scan)

Loader for 3d object

Parameters:

  • obj (object) – Loader object

  • line (int) – load, add, subtract line of object (indexing with 0)

  • scan (int) – number of the scan to be accessed

loadObj()

This method is not defined

plot(linewidth=4, title=None, xlabel=None, ylabel=None, ylabel_right=None, plot_height=450, plot_width=700, norm=False, waterfall=None, xprec=None, yprec=None, **kwargs)

Plot all data assosciated with class instance/object.

Parameters:

  • linewidth (int, optional)

  • title (string, optional)

  • xlabel (string, optional)

  • ylabel (string, optional)

  • ylabel_right (string, optional)

  • plot_height (int, optional)

  • plot_width (int, optional)

  • norm (boolean, optional) – Normalized plot output to [0,1]

  • waterfall (float) – Normalizes plot output to [0,1] and applies offset specified

  • xprec (int, optional) – Specifies the forced floating point X precision of the hover tool

  • yprec (int, optional) – Specifies the forced floating point Y precision of the hover tool

  • kwargs – all bokeh figure key-word arguments

plot_legend(pos)

Overwrite default legend position.

Parameters:

pos (string) – See bokeh manual for available options.

polygon(polygon, exact=False)

Mask array defined by a polygon and sum over specified axis

Parameters:

  • integration_axis (string) – options: ‘x’ or ‘y’

  • polygon (list of tuple) – corresponds to coordinate pairs

  • exact (Boolean) – True: Iterates over all data points P explicitly and determines if P is contained in polygon (most accurate, slow) False: Applies image algorithm to mask polygon by filling holes (less accurate, faster)

save_plot(fname, **kwargs)

Create a matplotlib plot window

fname: string

path and file name of the exported file

kwargs:
figsize: tuple

determines size of plot

x_minor_ticks: float

distance between minor ticks on primary axis

x_major_ticks: float

distance between major ticks on primary axis

y_minor_ticks: float

distance between minor ticks on secondary axis

y_major_ticks: float

distance between major ticks on secondary axis

top: Boolean

Display ticks on top of the plot

right: Boolean

Display ticks on the right of the plot

fontsize_axes: string or int

Set the fontsize of the axes ticks

fontsize_labels: string or int

Set fontsize of the axis labels

fontsize_title: string or int

Set fontsize of the title

title_pad: int

Padding between title and the top of the plot

xlabel: string

Label of the primary axis

ylabel: string

Label of the secondary axis

title: string

Title displayed at the top of the plot

xlim: tuple

Limits the visible x-range

ylim: tuple

Limits the visible y-range

legend: Boolean

Show/Hide plot legend

fontsize_legend: int

Fontsize of the legend entries

data_format: string, [pdf,svg,png]

Sets the output data format and matplotlib backend used

show_fluorescence(element, siegbahn_symbol, orientation='v', **kwargs)

Draw a line in the plot for the requested fluorescence line.

Parameters:

  • element (string) – IUPAC element abbreviation

  • siegbahn_symbol (string) – Siegbahn symbol for requested energy transition

  • orientation ([‘v’,’h’]) – Determines if a vertical or horizontal line is drawn

  • **kwargs (dict, optional) – See bokeh manual for available options.

stitch()

This method is not defined

subtract()

This method is not defined

vline(pos, **kwargs)

Draw a vertical line in the plot.

Parameters:

  • pos (float)

  • **kwargs (dict, optional) – See bokeh manual for available options.

xlim(lower, upper)

Set x-axis limits applied to data stream.

Parameters:

  • lower (float)

  • upper (float)

ylim(lower, upper)

Set y-axis limits applied to data stream.

Parameters:

  • lower (float)

  • upper (float)