pwem.viewers.viewer_coordinates module

class pwem.viewers.viewer_coordinates.CoordinateView(root, emSet: EMSet, protocol)

Bases: View

show()

This method should be overwritten to implement how this particular view will be displayed in desktop.

class pwem.viewers.viewer_coordinates.CoordinateViewer(tmpPath='./Tmp', **args)

Bases: Viewer

class pwem.viewers.viewer_coordinates.MainWindow(root, setOfCoordinate, protocol)

Bases: object

Coordinate viewer

addCoordinate(x, y, coordId=None)

Create a coordinate

applyBandpassFilter()

Apply the bandpass image filter

applyContrast()

applyGaussianBlur()

Apply the gaussian blur image filter

applyInvertContrast()

Invert the image contrast

applyPowerHistogram()

Create the histogram and the plot

calculateAveragePixel(shapeX, shapeY)

Calculate the shape pixel average

canPick(event)

Returns true if picking outside of any coordinate

clearImageGrid()

drawCoordinates(micId)

Draw the coordinates over the micrograph

drawRangeLines(ax, minVal, maxVal)

Draw vertical lines to represent the selected range

eraserActivate()

Recovering some actions when eraser button is pressed

extractImages()

Show the particles

extractRegion(x, y)

Take the particle region

filamentActivate()

Recovering some actions when filament button is pressed

getPixelValue(x, y)

Return the pixel value in the given x and y coordinates

histWindowClose()

histWindowSaveClose()

Save the new coordinates taking into account the sliders selected pixel range

isMoveIn(x, y)

loadCoordinates(micrograph)

Load the coordinate for a given micrograph

moveParticle(index)

nearCoordinates(index)

Calculate the near coordinates to a given coordinate

onBoxSizeSlider(event)

Handle box size slider motion

onClickPress(event)

Actions when the mouse left-click is pressed

onClickRelease(event)

Actions when the mouse left-click is released

onDrag(event)

Move the image and shapes on drag

onDragActivate()

Allow drag to move

onFitActivate()

Fit to display area and reset all parameters

onMotion(event)

Handle the eraser, picking filament and drag actions

onParticlesWindowClosing()

Close the particles window

onSliderMapMove(value)

onSliderRelease(event)

Handle box size slider release

onTableClick(event)

Handle the event when a row in the table is clicked to select a micrograph

onZoomActivate()

Allow zoom on scroll

onZoomImage(direction, event)

Zoom action

openFile()

Open a file dialog to load an image

pickingActivate()

Recovering some actions when picking button is pressed

plotHistogram(axes)

Plot the micrograph histogram

recoveryPointer(event)

Restoring the default cursor

removeCoordinates(value1, value2)

Remove the coordinate taking into account the pixel values

resetMicrograph()

Remove all coordinates from current micrograph

resizeRadious()

Calculate the shape radius taking into account the box size value

restoreMicrograph()

Restore all removed coordinates from current micrograph

selectCoordinate(event)

showCircles()

Draw a circle on the particle

showCoordinates()

Load and display the selected micrograph and coordinates

showPalette()

Color picker dialog

showParticles(geometry=None)

Create the particles window

showPoint()

Draw a point on the particle

showSquare()

Draw a square on the particle

updateImage(event)

Update the image with new size

updateParticle(index)

updateSize(event=None)

Update the size value label when the slider is moved

zoomerM(event)

Decrease size

zoomerP(event)

Increase size