unidec.metaunidec package

Subpackages

Submodules

unidec.metaunidec.image_plotter module

class unidec.metaunidec.image_plotter.ImagingWindow(*args, **kwargs)

Bases: Frame

Dialog window for Imaging.

extract(e=None, erange=None, dtype='mass', plot=None, no_face=False)
extract2(e=None)
extract3(e=None)
extract4(e=None)
image_plot(e=None, data=None, plot=None)
init(data, config=None)
init_data(data)
load(e=None)
load_plot1(e=None)
load_plot4(e=None)
on_cosine(event=None)
on_open_hdf5(e=None)
plot_mz_values(e=None)
sum_region(e=None)
update(e=None)

unidec.metaunidec.imzml_reader module

class unidec.metaunidec.imzml_reader.Imzml_Reader(path)

Bases: object

get_data()
write_to_hdf5(outfile=None)
unidec.metaunidec.imzml_reader.hdf5_to_imzml(path, outpath)
unidec.metaunidec.imzml_reader.imzml_to_hdf5(infile, outfile)

unidec.metaunidec.metafft module

class unidec.metaunidec.metafft.FFTWindow(parent, datalist, xvals=None, config=None, directory=None)

Bases: Frame

fft_process(e=None)
getfromgui()

Update parameters from GUI. :return: None

makeplot(e=None)

Runs the kendrick analysis on a single of the mass distributions in self.datalist set by self.pos. Plots the results in 1D and 2D. :return: None

on_add_line(e)

Add a horizontal line to the plot to visualize a predicted mass defect. Opens a dialog to input the value. Can be called more than once to add multiple lines. :param e: Unused event :return: None

on_close(e)

Close the window. Will try to set self.config.molig as self.m0. :param e: Unused event :return: None

on_save_fig(e)

Saves the figures in self.directory as PNGs. :param e: Unused event :return: None

on_save_fig_pdf(e)

Saves the figures in self.directory as PDFs. :param e: Unused event :return: None

unidec.metaunidec.mudeng module

class unidec.metaunidec.mudeng.MetaUniDec

Bases: UniDecEngine

batch_extract(paths)
batch_run_unidec(paths)
batch_set_config(paths)
clear()
combine_scanpeaks()
csv_reader(csvpath)
export_params(e=None)
export_spectra(e=None)
filter_peaks(minscore=0.4)
fit_data(fit='sig')
generate_image(peak_index=0)
import_mzml(paths, timestep=1.0, scanstep=None, starttp=None, endtp=None, name=None, startscan=None, endscan=None)

Tested :param paths: :param timestep: :return:

imzml_to_hdf5(infile, outfile)
make_grids()
normalize_exgrid()
open(path, speedy=False)
parse_file(p, timestep=None, scanstep=None, timepoint=None)

Tested :param p: :param timestep: :return:

parse_multiple_files(paths, starttp=None, endtp=None, timestep=1.0, name=None, startscan=None, endscan=None, scanstep=None)
peaks_error_replicates(pks, spectra, config)
peaks_heights()
pick_peaks(refresh=True)
pick_scanpeaks()
process_data()
run_unidec()
scanpeaks_extracts()
setup_filenames(path)
sum_masses(refresh=True)
write_to_imzML(outpath)
unidec.metaunidec.mudeng.metaunidec_call(config, *args, **kwargs)

unidec.metaunidec.mudhelp module

class unidec.metaunidec.mudhelp.HelpDlg(num, *args, **kw)

Bases: Frame

additional_filters()
additional_plotting()
animate_help()
auto_import_help()
auto_match_help()
autocorr_help()
baseline_help()
batch_help()
data_processing()
fft_help()
get_started()
import_window()
oligomer_help()
peak_selection()
peak_width_tool_help()
peak_window()
plot_window()
presets_help()
unidec_parameters()

unidec.metaunidec.mudstruct module

class unidec.metaunidec.mudstruct.MetaDataSet(engine)

Bases: object

add_data(data, name='', attrs=None, export=True)
add_file(filename=None, dirname=None, path=None)
attrs_to_df()
clear()
export_fits()
export_hdf5(file=None, vars_only=False, delete=False)
export_vars(file=None)
get_attr(attr)
get_bool()
get_colors()
get_max_data2()
get_spectra()
import_grids()
import_grids_and_peaks(refresh=True)
import_hdf5(file=None, speedy=False)
import_peaks()
import_vars(get_vnames=True, hdfobj=None)
new_file(path)
remove_data(indexes)
safemax(s)
update_var_array()
class unidec.metaunidec.mudstruct.Spectrum(topname, index, eng)

Bases: object

read_hdf5(file=None, speedy=False, hdfobj=None)
setup_peaks()
write_hdf5(file=None, vars_only=False, hdfobj=None)

unidec.metaunidec.mudview module

class unidec.metaunidec.mudview.Mainwindow(parent, title, config, iconfile=None, tabbed=None)

Bases: MainwindowBase

Main UniDec GUI Window.

export_gui_to_config()
setupmainpanel()
class unidec.metaunidec.mudview.MyFileDropTarget(window)

Bases: FileDropTarget

OnDropFiles(x, y, filenames)

When files are dropped, either open a single file or run in batch.

unidec.metaunidec.test_MUD module

class unidec.metaunidec.test_MUD.TestGUI(methodName='runTest')

Bases: TestCase

classmethod setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_auto_MS()
test_flip()
test_new_file()
test_presets_resets()
test_unidec_paths()

unidec.metaunidec.ultrameta module

class unidec.metaunidec.ultrameta.BarGraphWindow(parent, title, directory, *args, **kwargs)

Bases: Frame

on_exp_plot(fits=None, labels=None, errors=None, colors=None)
on_lin_plot(fits=None, labels=None, errors=None, colors=None)
on_save_figure_pdf(e)
on_save_figure_png(e, **kwargs)

Save all figures as PNG :param e: Dummy wx event :param kwargs: keywards to pass to matplotlib savefig :return: None

on_sig_plot(fits=None, labels=None, errors=None, colors=None)
save_all_figures(extension, e=0, header=None, **kwargs)

Save All of the Figures. Will name as header+extension2+_FigureX.+exetension :param extension: Figure type (pdf, eps, png). Anything accepted by matplotlib :param extension2: Additional text to include in the figure header. :param e: Dummy wx Event :param header: Option to add different header. Default of none yields self.outfname as the path header :param kwargs: Any keywards to pass to the matplotlib savefig command such as Transparent or DPI :return: figureflags, files (the figures that were successfully saved and the files that they were saved to)

setup_window(numplots=2)
setup_window_generic(xdim=1, ydim=1, type='1D')
class unidec.metaunidec.ultrameta.DataCollector(parent, title, config=None, *args, **kwargs)

Bases: Frame

load(savename)
load_params_from_hdf5(e=None, index=0)
load_x_from_peaks(e=None, index=0)
on_absolute_path(e)

Finished

on_add_x(e)
on_add_y(e)
on_bar_graphs(fits=None, labels=None, errors=None, fit=None, colors=None)
on_choose_dir(e)

Finished

on_exp_fit(e=None)
on_lab_frame(e=None)
on_lin_fit(e=None)
on_load(e)
on_local_path(e)

Finished

on_motion2(xpos, ypos)
on_plot_all(e=None, type='dist')
on_plot_all_MD(e=None)
on_run(e=None, fit=None, labframe=False)
on_save(e)
on_save_fig(e)

Finished

on_save_figPDF(e)

Finished

on_sig_fit(e=None)
on_ylabel(e)

Finished

open_file_in_meta(e=None, index=0)
run_hdf5(path)
update_config()
update_get(e=None)
update_gui()
update_hdf5(path)
update_set(e)
unidec.metaunidec.ultrameta.read_attr(thing, string, config)

Module contents