/
TractographyExportPLY.py
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TractographyExportPLY.py
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import os
import unittest
import vtk, qt, ctk, slicer
import numpy as np
from slicer.ScriptedLoadableModule import *
import logging
# helper class for cleaner multi-operation blocks on a single node.
class It(object):
def __init__(self, node): self.node = node
def __enter__(self): return self.node
def __exit__(self, type, value, traceback): return False
#
# TractographyExportPLY
#
class TractographyExportPLY(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
self.parent.title = "Export tractography to PLY (mesh)"
self.parent.categories = ["Diffusion.Import and Export"]
self.parent.dependencies = []
self.parent.contributors = ["Steve Pieper (Isomics, Inc.), Andras Lasso (Queen's University), Isaiah Norton (BWH)"]
self.parent.helpText = """
This module allows to export a tractography FiberBundleNode to an PLY or OBJ file for use with mesh editing/printing software.
"""
self.parent.helpText += self.getDefaultModuleDocumentationLink()
self.parent.acknowledgementText = """
This file was originally developed by Jean-Christophe Fillion-Robin, Kitware Inc.
and Steve Pieper, Isomics, Inc. and was partially funded by NIH grant 3P41RR013218-12S1.
Code updates and modularization by Andras Lasso and Isaiah Norton.
"""
#
# TractographyExportPLYWidget
#
class TractographyExportPLYWidget(ScriptedLoadableModuleWidget):
"""Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input volume selector
#
with It(slicer.qMRMLNodeComboBox()) as w:
self.inputSelector = w
w.nodeTypes = ["vtkMRMLFiberBundleNode"]
w.selectNodeUponCreation = True
w.addEnabled = False
w.removeEnabled = False
w.noneEnabled = False
w.showHidden = False
w.showChildNodeTypes = False
w.setMRMLScene( slicer.mrmlScene )
w.setToolTip( "Pick the fiber bundle to export." )
parametersFormLayout.addRow("Input FiberBundleNode: ", self.inputSelector)
#
# tube radius controller
#
with It(ctk.ctkSliderWidget()) as w:
self.radiusSelector = w
w.minimum = 0.1
w.maximum = 20.0
w.singleStep = 0.1
w.setToolTip("Select radius for output tubes")
parametersFormLayout.addRow("Tube radius: ", self.radiusSelector)
with It(ctk.ctkSliderWidget()) as w:
self.numSidesSelector = w
w.value = 6
w.decimals = 0
w.minimum = 3
w.maximum = 20
w.singleStep = 1
w.pageStep = 1
w.setToolTip("Select number of sides for output tube: higher number will look nicer, but will take more memory and time to export.")
parametersFormLayout.addRow("Number of sides: ", self.numSidesSelector)
#
# use native scalar range
#
with It(qt.QCheckBox()) as w:
self.nativeRangeCheckbox = w
w.checked = True
w.setToolTip("Checked: set the scalar range of the exported color table to match the scalar range of the selected node. Otherwise, the range will be set to [0,1].")
parametersFormLayout.addRow("Restrict scalar range", w)
#
# output file selector, export button, and status frame
#
with It(ctk.ctkPathLineEdit()) as w:
self.outputFileSelector = w
# make a file-only, save dialog
w.filters = ctk.ctkPathLineEdit.Files | ctk.ctkPathLineEdit.Writable
w.connect('currentPathChanged(const QString&)', self.reset)
parametersFormLayout.addRow("Output File: ", self.outputFileSelector)
with It(qt.QPushButton("Export")) as w:
self.exportButton = w
w.toolTip = "Run Export"
w.styleSheet = "background: lightgray"
w.connect('clicked(bool)', self.onExport)
parametersFormLayout.addRow("", w)
with It(qt.QStatusBar()) as w:
self.statusLabel = w
w.setToolTip("CLI status")
w.styleSheet = "background: lightgray"
parametersFormLayout.addRow("Status: ", w)
# Add vertical spacer
self.layout.addStretch(1)
def reset(self, _msg):
self.statusLabel.showMessage("")
def onExport(self):
self.statusLabel.showMessage("")
logic = TractographyExportPLYLogic()
res = False
try:
res = logic.exportFiberBundleToPLYPath(self.inputSelector.currentNode(),
self.outputFileSelector.currentPath,
radius = self.radiusSelector.value,
number_of_sides = self.numSidesSelector.value,
native_scalar_range = self.nativeRangeCheckbox.checked)
self.statusLabel.showMessage("Export succeeded!")
except Exception as err:
self.statusLabel.showMessage("ExportFailed: {}".format(err))
# note: use `raise` alone here, *not* `raise err` in order to
# get the full trace in the log and Python interactor.
raise
#
# TractographyExportPLYLogic
#
class TractographyExportPLYLogic(ScriptedLoadableModuleLogic):
def exportFiberBundleToPLYPath(self, inputFiberBundle, outputFilePath, radius = 0.5, number_of_sides = 6, native_scalar_range = False, outputCoordinateSystem = None):
"""
Export fiber bundle as colored tubes into PLY file.
outputCoordinateSystem: LPS or RAS. Default is LPS to match the most commonly image coordinate system.
"""
if outputCoordinateSystem is None:
outputCoordinateSystem = "LPS"
if not float(number_of_sides).is_integer():
import warnings
warnings.warn("Attempted inexact conversion for non-integer number_of_sides {}. This should never happen.".format(number_of_sides))
lineDisplayNode = inputFiberBundle.GetLineDisplayNode()
if lineDisplayNode is None:
raise Exception("No vtkMRMLFiberBundleLineDisplayNode found for node: {}".format(inputFiberBundle.GetName()))
outputDir = os.path.dirname(outputFilePath)
if not os.path.isdir(outputDir):
raise Exception("Selected output directory does not exist: {}".format(outputDir))
tuber = vtk.vtkTubeFilter()
tuber.SetNumberOfSides(int(number_of_sides))
tuber.SetRadius(radius)
tuber.SetInputData(lineDisplayNode.GetOutputPolyData())
tuber.Update()
tubes = tuber.GetOutputDataObject(0)
scalars = tubes.GetPointData().GetArray(0)
scalars.SetName("scalars")
triangles = vtk.vtkTriangleFilter()
triangles.SetInputData(tubes)
triangles.Update()
colorNode = lineDisplayNode.GetColorNode()
lookupTable = vtk.vtkLookupTable()
lookupTable.DeepCopy(colorNode.GetLookupTable())
if native_scalar_range:
scalarRange = lineDisplayNode.GetScalarRange()
lookupTable.SetTableRange(scalarRange[0], scalarRange[1])
else:
lookupTable.SetTableRange(0,1)
plyWriter = vtk.vtkPLYWriter()
if outputCoordinateSystem == "RAS":
plyWriter.SetInputData(triangles.GetOutput())
elif outputCoordinateSystem == "LPS":
transformRasToLps = vtk.vtkTransformPolyDataFilter()
rasToLps = vtk.vtkTransform()
rasToLps.Scale(-1, -1, 1)
transformRasToLps.SetTransform(rasToLps)
transformRasToLps.SetInputData(triangles.GetOutput())
plyWriter.SetInputConnection(transformRasToLps.GetOutputPort())
else:
raise RuntimeError("Invalid output coordinate system")
# Save coordinate system information in the file header
# (It allows reading of the
plyWriter.AddComment(f"3D Slicer output. SPACE={outputCoordinateSystem}")
if lineDisplayNode.GetColorMode() == lineDisplayNode.colorModeSolid:
# for solid colors we need to set uniform mode in the exporter,
# to avoid coloring by the last-used scalar array
plyWriter.SetColorModeToUniformPointColor()
color = np.array(np.multiply(lineDisplayNode.GetColor(), 255),
dtype=np.uint8) # range clamp
plyWriter.SetColor(color[0], color[1], color[2])
else:
plyWriter.SetLookupTable(lookupTable)
plyWriter.SetArrayName("scalars")
plyWriter.SetFileName(outputFilePath)
if (plyWriter.Write() == 0):
raise Exception("vtkPLYWriter return status: failed")
return True
class TractographyExportPLYTest(ScriptedLoadableModuleTest):
"""
This is the test case for your scripted module.
Uses ScriptedLoadableModuleTest base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def setUp(self):
""" Do whatever is needed to reset the state - typically a scene clear will be enough.
"""
slicer.mrmlScene.Clear(0)
def runTest(self):
"""Run as few or as many tests as needed here.
"""
self.setUp()
self.test_TractographyExportPLY1()
def test_TractographyExportPLY1(self):
self.delayDisplay("Starting the test")
try:
downloads = (
('fiber_ply_export_test', 'fiber_ply_export_test.vtk', 'https://github.com/SlicerDMRI/DMRITestData/blob/master/Tractography/fiber_ply_export_test.vtk?raw=true', 'FiberBundleFile'),
)
import SampleData
for nodeNames, fileNames, uris, loadFileTypes in downloads:
SampleData.downloadFromURL(
nodeNames=nodeNames,
fileNames=fileNames,
uris=uris,
loadFileTypes=loadFileTypes
)
self.delayDisplay('Finished with download and loading of %s' % str(fileNames))
# logic
outputPath = os.path.join(slicer.app.temporaryPath, "fiber.ply")
fiberNode = slicer.util.getNode(pattern="fiber_ply_export_test")
logic = TractographyExportPLYLogic()
logic.exportFiberBundleToPLYPath(fiberNode, outputPath, )
if not slicer.util.loadModel(outputPath):
raise Exception("Failed to load expected output PLY file: {}".format(outputPath))
# gui
outputPath2 = os.path.join(slicer.app.temporaryPath, "fiber2.ply")
widget = slicer.modules.TractographyExportPLYWidget
widget.inputSelector.setCurrentNode(fiberNode)
widget.outputFileSelector.currentPath = outputPath2
widget.exportButton.click()
if not slicer.util.loadModel(outputPath2):
raise Exception("Failed to load expected output PLY file: {}".format(outputPath2))
# If it doesn't throw, it passes...
self.delayDisplay('Test passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))