Documented functions with links to source

Program to plot parameters from segmented helices

class segmentplot.SegmentPlotPar

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_inp_spring_path
set_interactive_vs_batch_mode
set_quantities_to_be_plotted
set_set_size

define_parameters_and_their_properties()

define_program_states()

set_inp_spring_path(feature_set)

set_quantities_to_be_plotted(feature_set)

set_interactive_vs_batch_mode(feature_set)

set_set_size(feature_set)

class segmentplot.SegmentPlotPrepare(parset=None)

• Class that holds functions for examining segments from micrographs

• __init__ Function to interpret multi-input parameters

Methods

get_labels_according_to_quantities(set_size, …)

>>> from spring.segment2d.segmentplot import SegmentPlot

check_class_model_values_and_raise_error
check_class_values_and_raise_error
check_ctf_values_and_raise_error
check_layerline_values_and_raise_error
check_segmenting_values_and_raise_error
filter_segments_by_helix_and_micrograph_criteria
generate_set_id_label_for_plot_and_filename
get_plot_set
get_quantities_per_set
get_segment_ids_according_to_set_size
get_specified_quantities
get_subset_if_selected
prepare_helix_and_coordinates
prepare_log_string

check_class_values_and_raise_error(quantities, y_plot)

check_class_model_values_and_raise_error(quantities, y_plot)

check_ctf_values_and_raise_error(quantities, y_plot)

check_layerline_values_and_raise_error(quantities, y_plot)

check_segmenting_values_and_raise_error(quantities, y_plot)

get_subset_if_selected(plot_sets, attr_selection, attr_in_or_exclude, attr_entries, attr_id)

get_plot_set(set_size, obj)

filter_segments_by_helix_and_micrograph_criteria(session, obj)

prepare_helix_and_coordinates(set_size, quantities)

get_labels_according_to_quantities(set_size, quantities)

>>> from spring.segment2d.segmentplot import SegmentPlot
>>> SegmentPlot().get_labels_according_to_quantities('helix', 'coordinates') 
['Stack_id', 'X-Coordinate (Angstrom)', 'Y-Coordinate (Angstrom)', 'Picked X-Coordinate (Angstrom)', 
'Picked Y-Coordinate (Angstrom)']
>>> SegmentPlot().get_labels_according_to_quantities('helix', 'curvature') 
['Stack_id', 'Distance Along Helix (Angstrom)', 'Curvature', 'Selected Curvature']
>>> SegmentPlot().get_labels_according_to_quantities('data_set', 'curvature') 
['Stack_id', 'Curvature', 'Selected Curvature']
>>> SegmentPlot().get_labels_according_to_quantities('micrograph', 'astigmatism') 
['Stack_id', 'Astigmatism (Angstrom)', 'Selected Astigmatism (Angstrom)']

get_segment_ids_according_to_set_size(session, set_size, each_plot_set)

generate_set_id_label_for_plot_and_filename(set_size, each_plot_set)

get_specified_quantities(each_plot_set_string, set_size, quantities, xy_quantities, each_helix_stack_ids, each_helix_segments, overlapping_segments)

prepare_log_string(labels, xy_quantities)

get_quantities_per_set(spring_path, quantities)

class segmentplot.SegmentPlotVisualize(parset=None)

Methods

determine_position_of_point_within_frame(…)	>>> from spring.segment2d.segmentplot import SegmentPlot
get_labels_according_to_quantities(set_size, …)	>>> from spring.segment2d.segmentplot import SegmentPlot

add_avg_and_stdev_for_label
add_legend_at_best_location
add_stack_ids_to_upper_x_axis
check_class_model_values_and_raise_error
check_class_values_and_raise_error
check_ctf_values_and_raise_error
check_layerline_values_and_raise_error
check_segmenting_values_and_raise_error
choose_subplot_according_to_dimension
filter_segments_by_helix_and_micrograph_criteria
generate_set_id_label_for_plot_and_filename
get_plot_set
get_quantities_per_set
get_segment_ids_according_to_set_size
get_specified_quantities
get_subset_if_selected
make_distance_plot_including_histogram
plot_data_on_figure
plot_distance_along_y
plot_distance_along_y_including_local_average
plot_xy_coordinates
plot_y_histogram
prepare_helix_and_coordinates
prepare_log_string
print_progress_statement_if_interactive
set_legend_and_xlabel

determine_position_of_point_within_frame(frame_bottom_left, frame_top_right, x_quantity, y_quantity, x_lim, y_lim)

>>> from spring.segment2d.segmentplot import SegmentPlot
>>> s = SegmentPlot()
>>> x_quant = np.arange(5.0)
>>> y_quant = np.arange(5.0, 10.0)
>>> s.determine_position_of_point_within_frame([0.1, 0.2], [0.9, 0.8], x_quant, y_quant, (0.0, 4.0), (5.0, 9.0)) 
(array([0.1, 0.3, 0.5, 0.7, 0.9]), array([0.2       , 0.26666667, 0.33333333, 0.4       , 0.46666667]))

add_stack_ids_to_upper_x_axis(ax1, seg_ids, x_quantity, y_quantity, labels)

add_legend_at_best_location(ax1)

set_legend_and_xlabel(label, ax1)

plot_xy_coordinates(labels, set_id_label, xy_data, fig)

add_avg_and_stdev_for_label(y_quantity)

plot_y_histogram(labels, xy_data, set_size, fig)

make_distance_plot_including_histogram(diag_plot, labels, seg_ids, xy_data, set_size, fig, x_quantity, y_quantity, sel_y_quantity)

plot_distance_along_y_including_local_average(diag_plot, labels, seg_ids, xy_data, set_size, fig)

plot_distance_along_y(diag_plot, labels, seg_ids, xy_data, set_size, fig)

choose_subplot_according_to_dimension(diag_plot, labels, set_id_label, segid_xy, set_size, fig)

print_progress_statement_if_interactive(xy_quantities, batch_mode)

plot_data_on_figure(xy_quantities, labels)

class segmentplot.SegmentPlotGui(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)

class segmentplot.SegmentPlot(parset=None)

Methods

determine_position_of_point_within_frame(…)	>>> from spring.segment2d.segmentplot import SegmentPlot
get_labels_according_to_quantities(set_size, …)	>>> from spring.segment2d.segmentplot import SegmentPlot

add_avg_and_stdev_for_label
add_legend_at_best_location
add_stack_ids_to_upper_x_axis
check_class_model_values_and_raise_error
check_class_values_and_raise_error
check_ctf_values_and_raise_error
check_layerline_values_and_raise_error
check_segmenting_values_and_raise_error
choose_subplot_according_to_dimension
filter_segments_by_helix_and_micrograph_criteria
generate_set_id_label_for_plot_and_filename
get_plot_set
get_quantities_per_set
get_segment_ids_according_to_set_size
get_specified_quantities
get_subset_if_selected
launch_interactive_plot_gui
make_distance_plot_including_histogram
plot_data_on_figure
plot_desired_quantities
plot_distance_along_y
plot_distance_along_y_including_local_average
plot_xy_coordinates
plot_y_histogram
prepare_helix_and_coordinates
prepare_log_string
print_progress_statement_if_interactive
set_legend_and_xlabel

launch_interactive_plot_gui(feature_set, figures, tables, labels, hints=None)

plot_desired_quantities()

segmentplot.main()