lassoan

##################
## Written by: Kyle Sunderland
##
## Downloads all files from an assembla project
## Need to change repo_name, api_key, and api_secret for the script to work
##################

$repo_name = "REPO_NAME" # Name of the repo

# personal keys found at: https://app.assembla.com/user/edit/manage_clients

lassoan

# Important: the input volume must have isotropic spacing.
# If surface is thick, use Extract skeleton module with Skeleton type = 2D, Do not prune branches = enabled.
# Increase radius parameter to fill more holes.
# Increase dimension to preserve more details.

inputLabelmap = getNode('Input labelmap')

ici = vtk.vtkImageChangeInformation()
ici.SetInputData(inputLabelmap.GetImageData())
ici.SetOutputSpacing(inputLabelmap.GetSpacing())

lassoan

from __main__ import qt, slicer

#
# MarkupsInfo module
#

class MarkupsInfo:
  def __init__(self, parent):
    import string
    parent.title = "Markups info"

lassoan

def showSimpleUserInterface(simpleView):

    # Do not store these display settings permanently
    settings = qt.QSettings()
    settings.setValue('MainWindow/RestoreGeometry', not simpleView)

    for toolbar in slicer.util.mainWindow().findChildren('QToolBar'):
        toolbar.setVisible(not simpleView)

    modulePanelDockWidget = slicer.util.mainWindow().findChildren('QDockWidget','PanelDockWidget')[0]

lassoan

volumesDir = r"c:\Users\andra\OneDrive\Projects\SlicerTesting4\20190523-AutoWWWL\volumes"
screenshotsDir = r"c:\Users\andra\OneDrive\Projects\SlicerTesting4\20190523-AutoWWWL\screenshots"

methods = [
    ["baseline", autoContrastSlicerDefault],
    ["hist-0.1-99.9", lambda fn: autoContrastVtkImageHistogramStatisticsDefault(fn, 0.1, 99.9, 0.00, 0.0)], # = itksnap
    ["hist-1.0-99.9", lambda fn: autoContrastVtkImageHistogramStatisticsDefault(fn, 1.0, 99.9, 0.10, 0.0)],
    ["hist-1.0-99.0-x0.10", lambda fn: autoContrastVtkImageHistogramStatisticsDefault(fn, 1.0, 99.0, 0.10, 0.10)],
    ["hist-1.0-99.0-x0.20", lambda fn: autoContrastVtkImageHistogramStatisticsDefault(fn, 1.0, 99.0, 0.10, 0.20)],
    ]

lassoan

#
# Installation:
# - Save this file as AngleMeasurement.py to a directory on your computer
# - Add the directory to the additional module paths in the Slicer application settings:
#   - Choose in the menu: Edit / Application settings
#   - Click Modules, click >> next to Additional module paths
#   - Click Add, and choose the .py file's location
# - After you restart Slicer, "Angle Measurment" module should show up in Quantification category
#

lassoan

# Generate input data
################################################

import SampleData
import numpy as np

# Load master volume
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()

lassoan

import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
from array import array
import logging
import vtk.util.numpy_support
import numpy as np

#

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# Download a sample data set (chest CT)
import SampleData
masterVolumeNode = SampleData.SampleDataLogic().downloadCTChest()

# Create segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)

# Create temporary segment editor to get access to effects

lassoan

# Source data can be obtained from http://lifesciencedb.jp/bp3d/ (tested with partof_BP3D_4.0_obj_99)
# These input file must be loaded into the scene:
# - partof_inclusion_relation_list.txt and partof_element_parts.txt (loaded as Table nodes)
# - OBJ files

shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
sceneItemID = shNode.GetSceneItemID()

def getItemParentsFmaIds(shNode, itemShItemId):
    existingParentShItemId = shNode.GetItemParent(itemShItemId)