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mha_reader.py
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"""
Created on Wed Nov 7 16:23:58 2018
@author: domdo
"""
# External libraries
import os.path
import vtk
from vtk.util.numpy_support import vtk_to_numpy
import numpy as np
import random
def createMHAFileName(directory, count):
name_part1 = directory
name_part2 = "/%d.mha" %count
name = name_part1 + name_part2
return name
def returnDimsFirstImage(directory):
imageReader = vtk.vtkMetaImageReader()
imageReader.SetFileName(createMHAFileName(directory, 1))
imageReader.Update()
return imageReader.GetOutput().GetDimensions()
def returnSpacingFirstImage(directory):
imageReader = vtk.vtkMetaImageReader()
imageReader.SetFileName(createMHAFileName(directory, 1))
imageReader.Update()
return imageReader.GetOutput().GetSpacing()
def createVTKDataFromMHAFile(directory, count, interpolation, vtk_image_data_dimensions):
name = createMHAFileName(directory, count)
if os.path.isfile(name):
imageReader = vtk.vtkMetaImageReader()
imageReader.SetFileName(name)
imageReader.Update()
if interpolation == True:
resize = vtk.vtkImageResize()
resize.SetInputData(imageReader.GetOutput())
resize.SetOutputDimensions(vtk_image_data_dimensions)
resize.Update()
imageData1 = resize.GetOutput()
else:
imageData1 = imageReader.GetOutput()
return imageData1
def getNumberImages(directory):
counter = 1
name = createMHAFileName(directory, counter)
image_data_exists = True
while (image_data_exists):
if os.path.isfile(name):
counter = counter + 1
name = createMHAFileName(directory, counter)
else:
image_data_exists = False
return counter - 1
def return_matrix_image(image_name):
imr = vtk.vtkMetaImageReader()
imr.SetFileName(image_name)
imr.Update()
im = imr.GetOutput()
sc = im.GetPointData().GetScalars()
a = vtk_to_numpy(sc)
print (a.shape)
return a
def return_total_data_bin(directory):
count = 1
name = createMHAFileName(directory, count)
data_bin = np.array([])
while( os.path.isfile(name)):
data_bin = np.append(data_bin,return_matrix_image(name))
count = count + 1
name = createMHAFileName(directory, count)
return data_bin
def computeMinMax(directory):
count = 1
name = createMHAFileName(directory, 1)
min_ = np.amin(return_matrix_image(name))
max_ = np.amax(return_matrix_image(name))
while( os.path.isfile(name)):
if min_ < np.amin(return_matrix_image(name)):
min_ = np.amin(return_matrix_image(name))
if max_ < np.amax(return_matrix_image(name)):
max_ = np.amax(return_matrix_image(name))
count = count + 1
name = createMHAFileName(directory, count)
print("Min/Max:", min_, max_)
return [min_, max_]
def returnDataArray(directory, bool_create_histo, only_max_min, less_images):
data_bin = np.array([])
total_number_images = getNumberImages(directory)
if less_images is not None and total_number_images > less_images:
idx = random.sample(range(total_number_images), less_images)
idx_ = np.sort(idx)
for i in idx_:
print (" ",i)
name = createMHAFileName(directory, i)
data_bin = np.append(data_bin, return_matrix_image(name))
else:
if bool_create_histo == True:
data_bin = return_total_data_bin(directory)
else:
if only_max_min == True:
data_bin = np.array(computeMinMax(directory))
else:
data_bin = np.zeros(2)
return data_bin