pygmi.bholes package¶

Submodules¶

pygmi.bholes.coremask module¶

Core Mask Routines.

class pygmi.bholes.coremask.CoreMask(parent=None)¶

Bases: PyQt5.QtWidgets.QDialog

Core masking class.

change_defs()¶

Change definitions.

Returns
Return type: None.

classify()¶

Test classification.

Returns
Return type: None.

pic_overview()¶

Change the current viewed data, cased on the combo_overview value.

Returns
Return type: None.

pic_overview2()¶

Horizontal slider to change picture opacity.

Returns
Return type: None.

savemask()¶

Save mask to a file.

Returns
Return type: None.

settings(nodialog=False)¶

Entry point into item.

Returns: True if successful, False otherwise.
Return type: bool

setupui()¶

Set up UI.

Returns
Return type: None.

setwidth(width)¶

Set the width of the edits on the profile view.

Parameters: width (int) – Edit width.
Returns
Return type: None.

slayer()¶

Change model layer.

Returns
Return type: None.

class pygmi.bholes.coremask.MyMplCanvas(parent=None)¶

Bases: matplotlib.backends.backend_qt5agg.FigureCanvasQTAgg

Matplotlib Canvas.

button_press(event)¶

Button press event.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

button_release(event)¶

Button release event.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

init_grid_top(dat2=None, opac=100.0)¶

Initialise top grid.

Parameters

dat2 (str, optional) – Combobox text. The default is None.
opac (float, optional) – Opacity between 0 and 100. The default is 100.0.

Returns

Return type

None.

luttodat(dat)¶

LUT to dat grid.

Parameters: dat (numpy array) – Input array.
Returns: tmp – Output array.
Return type: numpy array

move(event)¶

Mouse move event.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

on_resize(event)¶

Resize event.

Used to make sure tight_layout happens on startup.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

set_mdata(xdata, ydata, mdata)¶

Routine to ‘draw’ the line on mdata.

xdata and ydata are the cursor centre coordinates.

Parameters

xdata (float) – X data.
ydata (float) – Y data.
mdata (numpy array) – Model array.

Returns

Return type

None.

slide_grid_top(opac=None)¶

Slide top grid.

Parameters: opac (float, optional) – Opacity between 0 and 100. The default is None.
Returns
Return type: None.

class pygmi.bholes.coremask.MySlider(parent=None)¶

Bases: PyQt5.QtWidgets.QSlider

My Slider.

Custom class which allows clicking on a horizontal slider bar with slider moving to click in a single step.

mouseMoveEvent(event)¶

Mouse move event.

Jump to pointer position while moving.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

mousePressEvent(event)¶

Mouse press event.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

pygmi.bholes.coremask.update_lith_lw(lith_list, mlut, lwidget)¶

Update the lithology list widget.

Parameters

lith_list (list) – Lithology list.
mlut (list) – Lithology color.
lwidget (QListWidget) – List widget.

Returns

Return type

None.

pygmi.bholes.coremeta module¶

Core metadata and depth Assignment routine.

class pygmi.bholes.coremeta.CoreMeta(parent=None)¶

Bases: PyQt5.QtWidgets.QDialog

Core metadata and depth assignment routine.

parent¶

reference to the parent routine

Type: parent

indata¶

dictionary of input datasets

Type: dictionary

outdata¶

dictionary of output datasets

Type: dictionary

button_press_callback(event)¶

Button press callback.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

dmark_change()¶

Change depth marker combo.

Returns
Return type: None.

dmark_del()¶

Delete depth marker.

Returns
Return type: None.

dmarkval_change()¶

Change depth marker value in spinbox.

Returns
Return type: None.

format_coord(x, y)¶

Format coordinate.

Parameters

x (float) – x-coordinate.
y (float) – y-coordinate.

Returns

Formatted string.

Return type

str

loadproj(projdata)¶

Load project data into class.

Parameters: projdata (dictionary) – Project data loaded from JSON project file.
Returns: chk – A check to see if settings was successfully run.
Return type: bool

ncore_change()¶

Routine is called when number of cores has changed.

Returns
Return type: None.

on_combo()¶

On combo.

Returns
Return type: None.

savedmark()¶

Save depth marks to a json file, with same name as the raster image.

Returns
Return type: None.

saveproj()¶

Save project data from class.

Returns: projdata – Project data to be saved to JSON project file.
Return type: dictionary

settings(nodialog=False)¶

Entrypoint into class.

Returns: True if successful, False otherwise.
Return type: bool

setupui()¶

Set up UI.

Returns
Return type: None.

traylen_change()¶

Routine is called whenever the tray length parameter is changed.

Returns
Return type: None.

update_depthfunc()¶

Update the depth function.

Returns
Return type: None.

class pygmi.bholes.coremeta.GraphMap(parent=None)¶

Bases: matplotlib.backends.backend_qt5agg.FigureCanvasQTAgg

Graph Map.

parent¶

reference to the parent routine

Type: parent

init_graph()¶

Initialise the graph.

Returns
Return type: None.

pygmi.bholes.graphs module¶

Plot Borehole Data.

This module provides a variety of methods to plot borehole data via the context menu.

class pygmi.bholes.graphs.GraphWindow(parent=None)¶

Bases: PyQt5.QtWidgets.QDialog

Graph Window.

parent¶

reference to the parent routine

Type: parent

change_band()¶

Combo box to change band.

Returns
Return type: None.

class pygmi.bholes.graphs.MyMplCanvas(parent=None)¶

Bases: matplotlib.backends.backend_qt5agg.FigureCanvasQTAgg

Canvas for the actual plot.

parent¶

reference to the parent routine

Type: parent

update_legend(data1)¶

Update legend.

Parameters: data1 (dictionary) – Dictionary containing data.
Returns
Return type: None.

update_log(data1)¶

Update the raster plot.

Parameters: data1 (dictionary.) – PyGMI log dataset to be used.
Returns
Return type: None.

class pygmi.bholes.graphs.PlotLog(parent=None)¶

Bases: pygmi.bholes.graphs.GraphWindow

Plot Log Class.

parent¶

reference to the parent routine

Type: parent

change_band()¶: Combo box to choose band.

run()¶

Run.

Returns
Return type: None.

pygmi.bholes.graphs.chkname(iname)¶

Check filename for illegal characters.

Parameters: iname (str) – Input filename.
Returns: iname – Corrected filename.
Return type: str

pygmi.bholes.graphs.commentprep(mystring, slen=50)¶

Create the correct case for a string and inserts carriage returns.

Parameters

mystring (str) – String to correct.
slen (int, optional) – String length. The default is 50.

Returns

finstring – Output string.

Return type

str

pygmi.bholes.graphs.gethatch(svgfile)¶

Get Hatching from SVG file.

Parameters: svgfile (str) – SVG filename.
Returns
Return type: None.

pygmi.bholes.hypercore module¶

Hyperspectral Core Routines.

class pygmi.bholes.hypercore.CorePrep(parent=None)¶

Bases: PyQt5.QtWidgets.QDialog

Tray clipping and band selection.

parent¶

reference to the parent routine

Type: parent

indata¶

dictionary of input datasets

Type: dictionary

outdata¶

dictionary of output datasets

Type: dictionary

acceptall()¶

Accept option.

Updates self.outdata, which is used as input to other modules.

Returns
Return type: None.

default_fenix()¶

Choose default settings for FENIX.

Returns
Return type: None.

default_owl()¶

Choose default settings for OWL.

Returns
Return type: None.

loadproj(projdata)¶

Load project data into class.

Parameters: projdata (dictionary) – Project data loaded from JSON project file.
Returns: chk – A check to see if settings was successfully run.
Return type: bool

on_combo()¶

On combo.

Returns
Return type: None.

saveproj()¶

Save project data from class.

Returns: projdata – Project data to be saved to JSON project file.
Return type: dictionary

settings(nodialog=False)¶

Entrypoint into class.

Returns: True if successful, False otherwise.
Return type: bool

setupui()¶

Set up UI.

Returns
Return type: None.

class pygmi.bholes.hypercore.GraphMap(parent=None)¶

Bases: matplotlib.backends.backend_qt5agg.FigureCanvasQTAgg

Graph Map.

parent¶

reference to the parent routine

Type: parent

init_graph()¶

Initialise the graph.

Returns
Return type: None.

update_graph()¶

Update graph.

Returns
Return type: None.

class pygmi.bholes.hypercore.ImageCor(parent=None)¶

Bases: PyQt5.QtWidgets.QDialog

Raw Imagery Corrections.

parent¶

reference to the parent routine

Type: parent

indata¶

dictionary of input datasets

Type: dictionary

outdata¶

dictionary of output datasets

Type: dictionary

acceptall()¶

Accept option.

Updates self.outdata, which is used as input to other modules.

Returns
Return type: None.

get_idir(dirname='')¶

Get input directory.

Parameters: filename (str, optional) – Directory name submitted for testing. The default is ‘’.
Returns
Return type: None.

get_odir(dirname='')¶

Get output directory.

Parameters: filename (str, optional) – Directory name submitted for testing. The default is ‘’.
Returns
Return type: None.

loadproj(projdata)¶

Load project data into class.

Parameters: projdata (dictionary) – Project data loaded from JSON project file.
Returns: chk – A check to see if settings was successfully run.
Return type: bool

saveproj()¶

Save project data from class.

Returns: projdata – Project data to be saved to JSON project file.
Return type: dictionary

settings(nodialog=False)¶

Entry point into item.

Returns: True if successful, False otherwise.
Return type: bool

setupui()¶

Set up UI.

Returns
Return type: None.

class pygmi.bholes.hypercore.PolygonInteractor(axtmp)¶

Bases: PyQt5.QtCore.QObject

Polygon Interactor.

button_press_callback(event)¶

Button press callback.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

button_release_callback(event)¶

Button release callback.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

draw_callback(event=None)¶

Draw callback.

Parameters: event (TYPE, optional) – DESCRIPTION. The default is None.
Returns
Return type: None.

epsilon = 5¶

motion_notify_callback(event)¶

Motion notify on mouse movement.

Parameters: event (TYPE) – DESCRIPTION.
Returns
Return type: None.

new_poly(npoly)¶

Routine for new polygon.

Parameters: npoly (list or None, optional) – New polygon coordinates.
Returns
Return type: None.

polyi_changed¶

set_line(xdata, ydata)¶

Routine to set line.

Parameters

xdata (float) – x coordinate.
ydata (float) – y coordinate data.

Returns

Return type

None.

showverts = True¶

update_plots()¶

Update plots.

Returns
Return type: None.

pygmi.bholes.hypercore.data_to_dict(dat)¶

Convert Data list to dictionary.

Parameters: dat (list of Data) – Input PyGMI dataset.
Returns: Output dictionary of data.
Return type: dictionary

pygmi.bholes.hypercore.dc_correct(idir, hfile, datah, piter=<built-in function iter>, showprocesslog=<built-in function print>)¶

DC Correct.

Parameters

idir (str) – Input directory.
hfile (str) – core filename.
datah (list of Data) – Input core data to be corrected.
piter (iter, optional) – Progress bar iterator. The default is iter.
showprocesslog (print, optional) – Default routine to show messages. The default is print.

Returns

Output Data.

Return type

list of Data

pygmi.bholes.hypercore.dict_to_data(arr, data)¶

Convert dictionary of Data to Data list.

Parameters

arr (dictionary) – Dictionary of raster datasets.
data (list of Data) – PyGMI Data to use as a template.

Returns

Output list of Data.

Return type

list of Data

pygmi.bholes.hypercore.dist_point_to_segment(p, s0, s1)¶

Dist point to segment.

Reimplementation of Matplotlib’s dist_point_to_segment, after it was depreciated. Follows http://geomalgorithms.com/a02-_lines.html

Parameters

p (numpy array) – Point.
s0 (numpy array) – Start of segment.
s1 (numpy array) – End of segment.

Returns

Distance of point to segment.

Return type

numpy array

pygmi.bholes.hypercore.filter_data(datah, ftype, piter=<built-in function iter>)¶

Filter data.

Parameters

datah (list of PyGMI Data) – Input data.
ftype (str) – Filter type. Can be hampel or savgol.

Returns

Output data.

Return type

list of PyGMI Data

pygmi.bholes.hypercore.hampel_filter(input_series, window_size, n_sigmas=3)¶

Hampel filter.

From https://towardsdatascience.com/outlier-detection-with-hampel-filter-85ddf523c73d

Parameters

input_series (numpy array) – Input series.
window_size (int) – Filter window size.
n_sigmas (int, optional) – Number of sigmas. The default is 3.

Returns

new_series (numpy array) – Output filtered series.
indices (numpy array) – Indices of values filtered.

pygmi.bholes.hypercore.smile(dat, piter=<built-in function iter>)¶

Geometric smile correction.

Parameters

dat (list of Data) – Input data to be corrected.
piter (iter, optional) – Progress bar iterator. The default is iter.

Returns

Output Data.

Return type

list of Data

pygmi.bholes.iodefs module¶

Import Borehole Data.

class pygmi.bholes.iodefs.ImportData(parent=None)¶

Bases: object

Import Data.

name¶

item name

Type: str

pbar¶

reference to a progress bar.

Type: progressbar

parent¶

reference to the parent routine

Type: parent

outdata¶

dictionary of output datasets

Type: dictionary

ifile¶

input file name. Used in main.py

Type: str

ext¶

filename extension

Type: str

loadproj(projdata)¶

Load project data into class.

Parameters: projdata (dictionary) – Project data loaded from JSON project file.
Returns: chk – A check to see if settings was successfully run.
Return type: bool

saveproj()¶

Save project data from class.

Returns: projdata – Project data to be saved to JSON project file.
Return type: dictionary

settings(nodialog=False)¶

Entry point into item.

Returns: True if successful, False otherwise.
Return type: bool

pygmi.bholes.iodefs.get_CGS(lithfile, headerfile)¶

Borehole Import.

Parameters

lithfile (str) – filename to import
headerfile (str) – filename to import

Returns

dat – dictionary of Pandas dataframes

Return type

dictionary

pygmi.bholes.menu module¶

Borehole Menu Routines.

class pygmi.bholes.menu.MenuWidget(parent=None)¶

Bases: object

Widget class to call the main interface.

This widget class creates the menus to be found on the main interface. Normal as well as context menus are defined here.

parent¶

Reference to MainWidget class found in main.py

Type: pygmi.main.MainWidget

coremask()¶: Core Masking.

coremeta()¶: Core Metadata and depth assignment.

coreprep()¶: Tray Clipping and Band Selection.

imagecor()¶: Raw core imagery corrections.

import_data()¶: Import data.

show_log()¶: Show log data.

Module contents¶

Borehole routines.

pygmi.bholes package¶

Submodules¶

pygmi.bholes.coremask module¶

pygmi.bholes.coremeta module¶

pygmi.bholes.graphs module¶

pygmi.bholes.hypercore module¶

pygmi.bholes.iodefs module¶

pygmi.bholes.menu module¶

Module contents¶

PyGMI

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