Documented functions with links to source

Program to simulate helical diffraction pattern and plot helical lattice from a series of indexed layer lines or rise/rotation parameters

class seglayer2lattice.SegLayer2LatticePar

Class to initiate default dictionary with input parameters including help and range values and status dictionary

Methods

define_parameters_and_their_properties
define_program_states
set_layer_bessel_or_symmetry
set_layer_bessel_or_symmetry_choice

define_parameters_and_their_properties()

define_program_states()

set_layer_bessel_or_symmetry(feature_set)

set_layer_bessel_or_symmetry_choice(feature_set)

class seglayer2lattice.SegLayer2LatticeGui(parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = Qt.WindowFlags())

Methods

PaintDeviceMetric	Attributes
RenderFlag	Attributes
RenderFlags(…)
acceptDrops(self)
accessibleDescription(self)
accessibleName(self)
actionEvent(self, QActionEvent)
actions(self)
activateWindow(self)
addAction(self, QAction)
addActions(self, object)
adjustSize(self)
autoFillBackground(self)
backgroundRole(self)
baseSize(self)
blockSignals(self, bool)
changeEvent(self, QEvent)
childAt(self, QPoint)	childAt(self, int, int) -> QWidget
childEvent(self, QChildEvent)
children(self)
childrenRect(self)
childrenRegion(self)
clearFocus(self)
clearMask(self)
close(self)
closeEvent(self, QCloseEvent)
colorCount(self)
connectNotify(self, QMetaMethod)
contentsMargins(self)
contentsRect(self)
contextMenuEvent(self, QContextMenuEvent)
contextMenuPolicy(self)
create(self, window, initializeWindow, …)
createWindowContainer(QWindow, parent, …)
cursor(self)
customContextMenuRequested	customContextMenuRequested(self, QPoint) [signal]
customEvent(self, QEvent)
deleteLater(self)
depth(self)
destroy(self, destroyWindow, destroySubWindows)
destroyed	destroyed(self, QObject = None) [signal]
devType(self)
devicePixelRatio(self)
devicePixelRatioF(self)
devicePixelRatioFScale()
disconnect(self)
disconnectNotify(self, QMetaMethod)
dragEnterEvent(self, QDragEnterEvent)
dragLeaveEvent(self, QDragLeaveEvent)
dragMoveEvent(self, QDragMoveEvent)
dropEvent(self, QDropEvent)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self)
effectiveWinId(self)
ensurePolished(self)
enterEvent(self, QEvent)
event(self, QEvent)
eventFilter(self, QObject, QEvent)
find(sip.voidptr)
findChild(self, type, name, options, …)	findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
findChildren(self, type, name, options, …)	findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
focusInEvent(self, QFocusEvent)
focusNextChild(self)
focusNextPrevChild(self, bool)
focusOutEvent(self, QFocusEvent)
focusPolicy(self)
focusPreviousChild(self)
focusProxy(self)
focusWidget(self)
font(self)
fontInfo(self)
fontMetrics(self)
foregroundRole(self)
frameGeometry(self)
frameSize(self)
geometry(self)
getContentsMargins(self)
grab(self, rectangle)
grabGesture(self, Qt.GestureType, flags, …)
grabKeyboard(self)
grabMouse(self) grabMouse(self, …)
grabShortcut(self, Union[QKeySequence, …)
graphicsEffect(self)
graphicsProxyWidget(self)
hasFocus(self)
hasHeightForWidth(self)
hasMouseTracking(self)
height(self)
heightForWidth(self, int)
heightMM(self)
hide(self)
hideEvent(self, QHideEvent)
inherits(self, str)
initPainter(self, QPainter)
inputMethodEvent(self, QInputMethodEvent)
inputMethodHints(self)
inputMethodQuery(self, Qt.InputMethodQuery)
insertAction(self, QAction, QAction)
insertActions(self, QAction, Iterable[QAction])
installEventFilter(self, QObject)
isActiveWindow(self)
isAncestorOf(self, QWidget)
isEnabled(self)
isEnabledTo(self, QWidget)
isFullScreen(self)
isHidden(self)
isLeftToRight(self)
isMaximized(self)
isMinimized(self)
isModal(self)
isRightToLeft(self)
isSignalConnected(self, QMetaMethod)
isVisible(self)
isVisibleTo(self, QWidget)
isWidgetType(self)
isWindow(self)
isWindowModified(self)
isWindowType(self)
keyPressEvent(self, QKeyEvent)
keyReleaseEvent(self, QKeyEvent)
keyboardGrabber()
killTimer(self, int)
layout(self)
layoutDirection(self)
leaveEvent(self, QEvent)
locale(self)
logicalDpiX(self)
logicalDpiY(self)
lower(self)
mapFrom(self, QWidget, QPoint)
mapFromGlobal(self, QPoint)
mapFromParent(self, QPoint)
mapTo(self, QWidget, QPoint)
mapToGlobal(self, QPoint)
mapToParent(self, QPoint)
mask(self)
maximumHeight(self)
maximumSize(self)
maximumWidth(self)
metaObject(self)
metric(self, QPaintDevice.PaintDeviceMetric)
minimumHeight(self)
minimumSize(self)
minimumSizeHint(self)
minimumWidth(self)
mouseDoubleClickEvent(self, QMouseEvent)
mouseGrabber()
mouseMoveEvent(self, QMouseEvent)
mousePressEvent(self, QMouseEvent)
mouseReleaseEvent(self, QMouseEvent)
move(self, QPoint) move(self, int, int)
moveEvent(self, QMoveEvent)
moveToThread(self, QThread)
nativeEvent(self, Union[QByteArray, bytes, …)
nativeParentWidget(self)
nextInFocusChain(self)
normalGeometry(self)
objectName(self)
objectNameChanged	objectNameChanged(self, str) [signal]
overrideWindowFlags(self, …)
overrideWindowState(self, …)
paintEngine(self)
paintEvent(self, QPaintEvent)
paintingActive(self)
palette(self)
parent(self)
parentWidget(self)
physicalDpiX(self)
physicalDpiY(self)
pos(self)
previousInFocusChain(self)
property(self, str)
pyqtConfigure(…)	Each keyword argument is either the name of a Qt property or a Qt signal.
raise_(self)
receivers(self, PYQT_SIGNAL)
rect(self)
releaseKeyboard(self)
releaseMouse(self)
releaseShortcut(self, int)
removeAction(self, QAction)
removeEventFilter(self, QObject)
render(self, QPaintDevice, targetOffset, …)
repaint(self) repaint repaint repaint(self, …)
resize(self, QSize) resize(self, int, int)
resizeEvent(self, QResizeEvent)
restoreGeometry(self, Union[QByteArray, …)
saveGeometry(self)
scroll(self, int, int) scroll(self, int, …)
sender(self)
senderSignalIndex(self)
setAcceptDrops(self, bool)
setAccessibleDescription(self, str)
setAccessibleName(self, str)
setAttribute(self, Qt.WidgetAttribute, on)
setAutoFillBackground(self, bool)
setBackgroundRole(self, QPalette.ColorRole)
setBaseSize(self, int, …)
setContentsMargins(self, int, int, int, …)
setContextMenuPolicy(self, Qt.ContextMenuPolicy)
setCursor(self, Union[QCursor, Qt.CursorShape])
setDisabled(self, bool)
setEnabled(self, bool)
setFixedHeight(self, int)
setFixedSize(self, QSize) setFixedSize(self, …)
setFixedWidth(self, int)
setFocus(self) setFocus(self, Qt.FocusReason)
setFocusPolicy(self, Qt.FocusPolicy)
setFocusProxy(self, QWidget)
setFont(self, QFont)
setForegroundRole(self, QPalette.ColorRole)
setGeometry(self, QRect) setGeometry(self, …)
setGraphicsEffect(self, QGraphicsEffect)
setHidden(self, bool)
setInputMethodHints(self, …)
setLayout(self, QLayout)
setLayoutDirection(self, Qt.LayoutDirection)
setLocale(self, QLocale)
setMask(self, QBitmap) setMask(self, QRegion)
setMaximumHeight(self, int)
setMaximumSize(self, int, …)
setMaximumWidth(self, int)
setMinimumHeight(self, int)
setMinimumSize(self, int, …)
setMinimumWidth(self, int)
setMouseTracking(self, bool)
setObjectName(self, str)
setPalette(self, QPalette)
setParent(self, QWidget) setParent(self, …)
setProperty(self, str, Any)
setShortcutAutoRepeat(self, int, enabled)
setShortcutEnabled(self, int, enabled)
setSizeIncrement(self, int, …)
setSizePolicy(self, …)
setStatusTip(self, str)
setStyle(self, QStyle)
setStyleSheet(self, str)
setTabOrder(QWidget, QWidget)
setToolTip(self, str)
setToolTipDuration(self, int)
setUpdatesEnabled(self, bool)
setVisible(self, bool)
setWhatsThis(self, str)
setWindowFilePath(self, str)
setWindowFlags(self, Union[Qt.WindowFlags, …)
setWindowIcon(self, QIcon)
setWindowIconText(self, str)
setWindowModality(self, Qt.WindowModality)
setWindowModified(self, bool)
setWindowOpacity(self, float)
setWindowRole(self, str)
setWindowState(self, Union[Qt.WindowStates, …)
setWindowTitle(self, str)
sharedPainter(self)
show(self)
showEvent(self, QShowEvent)
showFullScreen(self)
showMaximized(self)
showMinimized(self)
showNormal(self)
signalsBlocked(self)
size(self)
sizeHint(self)
sizeIncrement(self)
sizePolicy(self)
stackUnder(self, QWidget)
startTimer(self, int, timerType)
statusTip(self)
style(self)
styleSheet(self)
tabletEvent(self, QTabletEvent)
testAttribute(self, Qt.WidgetAttribute)
thread(self)
timerEvent(self, QTimerEvent)
toolTip(self)
toolTipDuration(self)
tr(self, str, disambiguation, n)
underMouse(self)
ungrabGesture(self, Qt.GestureType)
unsetCursor(self)
unsetLayoutDirection(self)
unsetLocale(self)
update(self) update update update(self, int, …)
updateGeometry(self)
updateMicroFocus(self)
updatesEnabled(self)
visibleRegion(self)
whatsThis(self)
wheelEvent(self, QWheelEvent)
width(self)
widthMM(self)
winId(self)
window(self)
windowFilePath(self)
windowFlags(self)
windowHandle(self)
windowIcon(self)
windowIconChanged	windowIconChanged(self, QIcon) [signal]
windowIconText(self)
windowIconTextChanged	windowIconTextChanged(self, str) [signal]
windowModality(self)
windowOpacity(self)
windowRole(self)
windowState(self)
windowTitle(self)
windowTitleChanged	windowTitleChanged(self, str) [signal]
windowType(self)
x(self)
y(self)

add_tab_with_new_symmetry
build_controls
build_figure
changeInputChoice
get_parameters_from_dict
get_title_for_current_tab
open_another_tab
turn_rot_sym_dial_on_or_off

enterEvent(self, QEvent)

get_parameters_from_dict()

build_figure()

build_controls()

turn_rot_sym_dial_on_or_off(state)

changeInputChoice(choice)

open_another_tab()

get_title_for_current_tab()

add_tab_with_new_symmetry()

class seglayer2lattice.SegLayer2LatticePreparation(parset=None)

• Class that holds functions for plotting assigned layer lines to helical lattice

Methods

convert_entry_to_rise_rotation_pair(entry)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
prepare_layerline_bessel_pairs_from_list(…)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice

prepare_layerline_bessel_pairs_from_list(layerlines, bessel_orders)

>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
>>> s = SegLayer2Lattice()
>>> positions = '0.123, 0.234, 0.345'
>>> s.prepare_layerline_bessel_pairs_from_list(positions, '-2, 4, 5')
[(0.123, -2), (0.234, 4), (0.345, 5)]
 >>> s.prepare_layerline_bessel_pairs_from_list(positions, '-2, 4') 
 Traceback (most recent call last):
  File '<stdin>', line 1, in <module>
  File 'spring/segment2d/seglayer2lattice.py', line 85, in 
      prepare_layerline_bessel_pairs_from_list
    raise ValueError, error_message
 ValueError: Number of layer line positions does not equal number of 
     assigned Bessel orders. Please revise.
 >>> s.prepare_layerline_bessel_pairs_from_list('0.123', '-2 4') 
 Traceback (most recent call last):
  File '<stdin>', line 1, in <module>
  File 'spring/segment2d/seglayer2lattice.py', line 77, in 
      prepare_layerline_bessel_pairs_from_list
    raise ValueError, error_message
 ValueError: No comma-separated list was detected. Please check 
     input of layer line positions.

convert_entry_to_rise_rotation_pair(entry)

>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
>>> s = SegLayer2Lattice()
>>> s.convert_entry_to_rise_rotation_pair('1.408, 22.03')
(1.408, 22.03)

class seglayer2lattice.SegLayer2LatticePlot(parset=None)

Methods

convert_entry_to_rise_rotation_pair(entry)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
determine_number_of_lattice_lines_required_for_plot(…)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
prepare_layerline_bessel_pairs_from_list(…)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice

filter_layer_line_bessel_pairs_to_10A_and_150A_resolution
generate_lattice_line
include_lattice_lines_in_plot
limit_to_a_maximum_of_ten_for_display
plot_helical_lattice
set_up_general_lattice_plot_properties

generate_lattice_line(pitch_bessel_pair, lines_count)

determine_number_of_lattice_lines_required_for_plot(layerline_bessel_pairs)

>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
>>> s = SegLayer2Lattice()
>>> s.determine_number_of_lattice_lines_required_for_plot([(0.123, -2), (0.234, 4), (0.35, 5)])
84

include_lattice_lines_in_plot(layerline_bessel_pairs, ax1, lines_count)

set_up_general_lattice_plot_properties(ax, maximum_pitch)

limit_to_a_maximum_of_ten_for_display(layerline_bessel_pairs)

filter_layer_line_bessel_pairs_to_10A_and_150A_resolution(layerline_bessel_pairs)

plot_helical_lattice(layerline_bessel_pairs, ax2)

class seglayer2lattice.SegLayer2LatticeMontage(parset=None)

Methods

convert_entry_to_rise_rotation_pair(entry)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
determine_number_of_lattice_lines_required_for_plot(…)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
prepare_layerline_bessel_pairs_from_list(…)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice

filter_layer_line_bessel_pairs_to_10A_and_150A_resolution
generate_lattice_line
histeq
include_lattice_lines_in_plot
limit_to_a_maximum_of_ten_for_display
plot_helical_lattice
set_up_general_lattice_plot_properties

histeq(em_img, nbr_bins=65535)

class seglayer2lattice.SegLayer2Lattice(parset=None)

Methods

convert_entry_to_rise_rotation_pair(entry)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
determine_number_of_lattice_lines_required_for_plot(…)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice
prepare_layerline_bessel_pairs_from_list(…)	>>> from spring.segment2d.seglayer2lattice import SegLayer2Lattice

compute_layer_line_bessel_pairs
filter_layer_line_bessel_pairs_to_10A_and_150A_resolution
format_second_layer_line_plot
format_ticklabels_to_six_and_xlabel_to_eight
generate_lattice_line
get_layer_line_bessel_pairs
histeq
include_lattice_lines_in_plot
launch_seglayer2lattice_gui
limit_to_a_maximum_of_ten_for_display
plot_helical_lattice
plot_layer_lines_in_power_spectrum
plot_layer_lines_to_power_and_lattice
prepare_layer_line_plot
print_seglayer2lattice
set_up_general_lattice_plot_properties

compute_layer_line_bessel_pairs(layer_bessel_or_sympair_choice, layer_sympair_entry, helixwidth, pixelsize, high_res_cutoff, low_res_cutoff, rotational_sym)

format_ticklabels_to_six_and_xlabel_to_eight(ax2)

format_second_layer_line_plot(ax2, line)

get_layer_line_bessel_pairs()

prepare_layer_line_plot(layerline_bessel_pairs, ax2, linex_fine)

plot_layer_lines_in_power_spectrum(layerline_bessel_pairs, ax1, ax2)

print_seglayer2lattice()

launch_seglayer2lattice_gui(feature_set)

plot_layer_lines_to_power_and_lattice()

seglayer2lattice.main()