tomo3D.viewers.viewer_mrc module

class tomo3D.viewers.viewer_mrc.LoadingScreen

Bases: PyQt5.QtWidgets.QWidget

startAnimation()

stopAnimation()

class tomo3D.viewers.viewer_mrc.MrcPlot(tomo_mrc=None, mask_mrc=None, points=None, boxSize=None, normals=None, binning=None, sigma=1.0, triangulation=False)

Bases: object

Class to visualize MRC files Input paramters:

• tomo_mrc (Path (Str) - Optional): File containing a Volume (in MRC format)
• mask_mrc (Path (Str) - Optional): File containing a Mask (in MRC format)
• points (Path (Str) - Optional): File containing a SetOfCoordinates3D (in TEXT format)
• boxSize (Double - Optional): Box size associated to points
• normals (Path (Str) - Optional): File containing a Set of Normals (in TEXT format)
• binning (Float - Optional): Binning factor to be applied to tomo_mrc and mask_mrc (Very useful to save time)
• sigma (Float - Optional): Gaussian Filter width
• triangulation (Bool - Optional): Tells if the representation of the Tomogram is Voxel based on Triangle based

Usage:

import MRCPlot plt = MRCPlot(tomo_mrc=tomo_mrc, mask_mrc=mask_mrc, binning=2) plt.initializePlot()

contours(hist, bin_centers)

downsamplingPC(coords, voxel_size)

getBinning(file)

gridFromMRC(data)

Function to convert an MRC file into an Structure Grid in VTK

histogram(volume)

initializePlot()

isovolumes(volume, range=0.01, sigma=None, triangulation=True)

loadInMemory(source, sliceMode=False)

marchingCubes(volume, level=None, triangulation=True)

plotBoxes(value)

plotMasks(value)

plotNormals(value)

plotPoints(value)

plotTomo(value)

readMRC(file, binning=1, order=0, swapaxes=True)

showMask(load=True)

showSlices(load=True)

showTomogram(load=True)

surfaceFromMRC(data, label=1)

Function to convert an MRC file into an Structure Surface in VTK

toogleSlice(value)

class tomo3D.viewers.viewer_mrc.Worker(viewer)

Bases: PyQt5.QtCore.QObject

finished

runMaskLoading()

runTomoLoading()