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############################################################################
#
# Program: GDCM (Grassroots DICOM). A DICOM library
#
# Copyright (c) 2006-2011 Mathieu Malaterre
# All rights reserved.
# See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
#
# This software is distributed WITHOUT ANY WARRANTY; without even
# the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the above copyright notice for more information.
#
############################################################################
# This used to be important to load the vtkgdcm module first
# (VTK 5.2 contains the proper patch now)
import vtkgdcm
from vtkgdcm import vtkStringArray
from vtk.util import vtkConstants as vtkType
import gdcm # for gdcm.Directory
import os,sys
def PrintProgress(object, event):
assert event == "ProgressEvent"
print("Progress:", object.GetProgress())
if __name__ == "__main__":
root = gdcm.Testing.GetDataExtraRoot()
dirname = os.path.join(root, "gdcmSampleData/ForSeriesTesting/Perfusion/images" )
print(dirname)
# setup reader
r = vtkgdcm.vtkGDCMThreadedImageReader2()
dir = gdcm.Directory()
# Did user pass in a directory:
system = gdcm.System()
if system.FileIsDirectory( dirname ):
nfiles = dir.Load( dirname )
files = dir.GetFilenames()
# Need to construct full path out of the simple filename
fullpath = vtkStringArray()
for file in files:
fullpath.InsertNextValue( file )
r.SetFileNames( fullpath )
assert fullpath.GetNumberOfValues() # Need at least one file
# Now specify the property of the image:
"""
Note (MM), I verified that even if there are multiple Series in this Study they are all compatible and thus
can be loaded as a fake 3D (VTK) volume, only origin is changing & shift/scale .
See:
$ for i in `ls ForSeriesTesting/Perfusion/images/1.*`; do gdcminfo $i; done | sort | uniq
"""
"""
gdcminfo ForSeriesTesting/Perfusion/images/1.3.46.670589.5.2.14.2198403904.1100092395.157798.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
NumberOfDimensions: 2
Dimensions: (256,256)
Origin: (-115,-125.969,-17.068)
Spacing: (0.898438,0.898438,5.5)
DirectionCosines: (1,0,0,0,0.949631,-0.31337)
Rescale Intercept/Slope: (-1985.36,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
Orientation Label: AXIAL
"""
dims = [0,0,0]
dims[0] = 256
dims[1] = 256
dims[2] = nfiles
# Even if Stored Pixel is UINT16, the World Value Pixel is Float
datascalartype = vtkType.VTK_FLOAT
spacing = [0.898438,0.898438,5.5]
origin = [-115,-125.969,-17.068]
intercept_slope = [-1985.36,1]
numberOfScalarComponents = 1
r.SetDataExtent( 0, dims[0] - 1, 0, dims[1] - 1, 0, dims[2] - 1 )
r.SetDataScalarType ( datascalartype )
r.SetNumberOfScalarComponents( numberOfScalarComponents )
r.SetDataOrigin( origin )
r.SetDataSpacing( spacing )
# Useless only for backward compatibility, the real shift/scale will be read from files:
#r.SetShift( intercept_slope[0] )
#r.SetScale( intercept_slope[1] )
# Setup the ProgressEvent
r.AddObserver("ProgressEvent", PrintProgress)
r.Update()
print(r.GetOutput())
# Test succeed ?
#sys.exit(success != 1)
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