# Dicom Series Read Modify Write¶

## Overview¶

This example illustrates how to read a DICOM series, modify the 3D image, and then write the result as a DICOM series.

Reading the DICOM series is a three step process: first obtain the series ID, then obtain the file names associated with the series ID, and finally use the series reader to read the images. By default the DICOM meta-data dicitonary for each of the slices is not read. In this example we configure the series reader to load the meta-data dictionary including all of the private tags.

Modifying the 3D image can involve changes to its physical charecteristics (spacing, direction cosines) and its intensities. In our case we only modify the intensities by blurring the image.

Writing the 3D image as a DICOM series is done by configuring the meta-data dictionary for each of the slices and then writing it in DICOM format. In our case we copy some of the meta-data from the original dictionaries which are available from the series reader. We then set some additional meta-data values to indicate that this series is derived from the original acquired data. Note that we write the intensity values as is and thus do not set the rescale slope (0028|1053), rescale intercept (0028|1052) meta-data dictionary values.

## Code¶

from __future__ import print_function

import SimpleITK as sitk

import sys
import time
import os

if len(sys.argv) < 3:
print("Usage: python " + __file__ +
" <input_directory_with_DICOM_series> <output_directory>")
sys.exit(1)

# Read the original series. First obtain the series file names using the
data_directory = sys.argv[1]
if not series_IDs:
print("ERROR: given directory \"" + data_directory +
"\" does not contain a DICOM series.")
sys.exit(1)
data_directory, series_IDs[0])

# Configure the reader to load all of the DICOM tags (public+private):
# By default tags are not loaded (saves time).
# By default if tags are loaded, the private tags are not loaded.
# private ones.

# Modify the image (blurring)
filtered_image = sitk.DiscreteGaussian(image3D)

# Write the 3D image as a series
# IMPORTANT: There are many DICOM tags that need to be updated when you modify
#            an original image. This is a delicate opration and requires
#            knowledge of the DICOM standard. This example only modifies some.
#            For a more complete list of tags that need to be modified see:
#                http://gdcm.sourceforge.net/wiki/index.php/Writing_DICOM

writer = sitk.ImageFileWriter()
# Use the study/series/frame of reference information given in the meta-data
# dictionary and not the automatically generated information from the file IO
writer.KeepOriginalImageUIDOn()

# Copy relevant tags from the original meta-data dictionary (private tags are
# also accessible).
tags_to_copy = ["0010|0010",  # Patient Name
"0010|0020",  # Patient ID
"0010|0030",  # Patient Birth Date
"0020|000D",  # Study Instance UID, for machine consumption
"0020|0010",  # Study ID, for human consumption
"0008|0020",  # Study Date
"0008|0030",  # Study Time
"0008|0050",  # Accession Number
"0008|0060"  # Modality
]

modification_time = time.strftime("%H%M%S")
modification_date = time.strftime("%Y%m%d")

# Copy some of the tags and add the relevant tags indicating the change.
# For the series instance UID (0020|000e), each of the components is a number,
# cannot start with zero, and separated by a '.' We create a unique series ID
# using the date and time.
# Tags of interest:
direction = filtered_image.GetDirection()
series_tag_values = [
for k in tags_to_copy
[("0008|0031", modification_time),  # Series Time
("0008|0021", modification_date),  # Series Date
("0008|0008", "DERIVED\\SECONDARY"),  # Image Type
("0020|000e", "1.2.826.0.1.3680043.2.1125." +
modification_date + ".1" + modification_time),
# Series Instance UID
("0020|0037",
'\\'.join(map(str, (direction[0], direction[3],
direction[6],
# Image Orientation (Patient)
direction[1], direction[4],
direction[7])))),
("0008|103e",
+ " Processed-SimpleITK")]  # Series Description

for i in range(filtered_image.GetDepth()):
image_slice = filtered_image[:, :, i]
# Tags shared by the series.
for tag, value in series_tag_values:
# Slice specific tags.
#   Instance Creation Date
#   Instance Creation Time
#   Image Position (Patient)
map(str, filtered_image.TransformIndexToPhysicalPoint((0, 0, i)))))
#   Instace Number

# Write to the output directory and add the extension dcm, to force writing
# in DICOM format.
writer.SetFileName(os.path.join(sys.argv[2], str(i) + '.dcm'))
writer.Execute(image_slice)
sys.exit(0)

library(SimpleITK)

args <- commandArgs( TRUE )

if (length(args) < 2) {
write("Usage arguments: <input_directory_with_DICOM_series> <output_directory>", stderr())
quit(save="no", status=1)
}

# Read the original series. First obtain the series file names using the
data_directory <- args[1]
if(length(series_IDs)==0) {
write(paste0("ERROR: given directory \"",data_directory,"\" does not contain a DICOM series."))
quit(save="no", status=1)
}

series_reader$SetFileNames(series_file_names) # Configure the reader to load all of the DICOM tags (public+private): # By default tags are not loaded (saves time). # By default if tags are loaded, the private tags are not loaded. # We explicitly configure the reader to load tags, including the # private ones. series_reader$MetaDataDictionaryArrayUpdateOn()
series_reader$LoadPrivateTagsOn() image3D <- series_reader$Execute()

# Modify the image (blurring)
filtered_image <- DiscreteGaussian(image3D)

# Write the 3D image as a series
# IMPORTANT: There are many DICOM tags that need to be updated when you modify an
#            original image. This is a delicate opration and requires knowlege of
#            the DICOM standard. This example only modifies some. For a more complete
#            list of tags that need to be modified see:
#                           http://gdcm.sourceforge.net/wiki/index.php/Writing_DICOM

writer <- ImageFileWriter()
# Use the study/series/frame of reference information given in the meta-data
# dictionary and not the automatically generated information from the file IO
writer$KeepOriginalImageUIDOn() # Copy relevant tags from the original meta-data dictionary (private tags are also # accessible). tags_to_copy <- c("0010|0010", # Patient Name "0010|0020", # Patient ID "0010|0030", # Patient Birth Date "0020|000D", # Study Instance UID, for machine consumption "0020|0010", # Study ID, for human consumption "0008|0020", # Study Date "0008|0030", # Study Time "0008|0050", # Accession Number "0008|0060" # Modality ) modification_time <- format(Sys.time(), "%H%M%S") modification_date <- format(Sys.time(), "%Y%m%d") # Copy some of the tags and add the relevant tags indicating the change. # When attempting to copy we are not ensured that the tags exist, in which case # we get a NULL as an entry in the list returned by lapply, these are removed # by the Filter. # For the series instance UID (0020|000e), each of the components is a number, cannot start # with zero, and separated by a '.' We create a unique series ID using the date and time. # tags of interest: direction <- filtered_image$GetDirection()
series_tag_values <- c(Filter(Negate(is.null),
lapply(tags_to_copy,
function(k) {
if(series_reader$HasMetaDataKey(0,k)) { list(k, series_reader$GetMetaData(0,k))
}
})),
list(list("0008|0031",modification_time), # Series Time
list("0008|0021",modification_date), # Series Date
list("0008|0008","DERIVED\\SECONDARY"), # Image Type
list("0020|000e", paste0("1.2.826.0.1.3680043.2.1125.",modification_date,".1",modification_time)), # Series Instance UID
list("0020|0037", paste(c(direction[1], direction[4], direction[7],
direction[2],direction[5],direction[8]), collapse="\\")), # Image Orientation (Patient)
list("0008|103e", paste0(series_reader$GetMetaData(0,"0008|103e"), " Processed-SimpleITK")))) # Series Description for(i in 1:filtered_image$GetDepth()) {
image_slice <- filtered_image[,,i]
# Tags shared by the series.
invisible(lapply(series_tag_values,
function(tag_value) {image_slice$SetMetaData(tag_value[1], tag_value[2])})) # Slice specific tags. image_slice$SetMetaData("0008|0012", format(Sys.time(), "%Y%m%d")) # Instance Creation Date
image_slice$SetMetaData("0008|0013", format(Sys.time(), "%H%M%S")) # Instance Creation Time image_slice$SetMetaData("0020|0032", paste(filtered_image$TransformIndexToPhysicalPoint(c(0,0,i-1)), collapse="\\")) # Image Position (Patient) image_slice$SetMetaData("0020|0013", as.character(i)) # Instance Number

# Write to the output directory and add the extension dcm, to force writing in DICOM format.
writer$SetFileName(file.path(args[[2]], sprintf("%d.dcm",i))) writer$Execute(image_slice)
}

quit(save="no", status=0)