DICOM Instance Class

An abstract class for a DICOM Instance resource.

Value

An R6 instance of class "Instance".

Super class

orthanc::Resource -> Instance

Active bindings

uid

SOPInstanceUID

file_size

File size

creation_date

Creation Date

series_identifier

Parent series identifier

parent_series

Parent series

parent_study

Parent study

parent_patient

Parent patient

acquisition_number

Acquisition Number

image_index

Image Index

image_orientation_patient

Image Orientation Patient

image_position_patient

Image Position Patient

image_comments

Image Comments

instance_number

Instance Number

temporal_position_identifier

Temporal Position Identifier

tags

Tags

simplified_tags

Simplified Tags

labels

Get or add labels

statistics

Statistics

list_frames

List frames (zero-based indexing)

frames

Number of frames

rows

Number of rows

columns

Number of columns

shape

Shape (rows x columns x frames (if multi-frame))

dim

Number of dimensions

slice_thickness

Slice thickness

pixel_spacing

Pixel spacing

Methods

Public methods

• Instance$get_dicom_file_content()

• Instance$download_dicom()

• Instance$get_main_information()

• Instance$add_label()

• Instance$has_label()

• Instance$remove_label()

• Instance$get_raw_content_by_tag()

• Instance$anonymize()

• Instance$modify()

• Instance$get_nifti_file_content()

• Instance$download_nifti()

• Instance$download_image()

• Instance$clone()

Inherited methods

• orthanc::Resource$initialize()
• orthanc::Resource$print()
• orthanc::Resource$set_child_resources()

---

Method get_dicom_file_content()

Retrieves bytes of DICOM file content

This method retrieves bytes corresponding to the DICOM file.

Usage

Instance$get_dicom_file_content()

---

Method download_dicom()

Download DICOM file to a path.

Usage

Instance$download_dicom(path, stream = FALSE)

Arguments

path

Path on disk.

stream

Should the resource be streamed and written to disk in chunks? Default is FALSE, which means the resource file contents are retrieved in their entirety and written to disk all at once.

---

Method get_main_information()

Get instance information.

Usage

Instance$get_main_information()

---

Method add_label()

Add label to resource.

Usage

Instance$add_label(label)

Arguments

label

Label.

---

Method has_label()

Test if resource has label.

Usage

Instance$has_label(label)

Arguments

label

Label.

---

Method remove_label()

Delete label from resource.

Usage

Instance$remove_label(label)

Arguments

label

Label.

---

Method get_raw_content_by_tag()

Get raw content of one DICOM tag.

Usage

Instance$get_raw_content_by_tag(tag)

Arguments

tag

tag.

---

Method anonymize()

Anonymize Instance

Usage

Instance$anonymize(
  remove = list(),
  replace = list(),
  keep = list(),
  keep_private_tags = FALSE,
  keep_source = TRUE,
  private_creator = NULL,
  force = FALSE,
  dicom_version = NULL
)

Arguments

remove

List of tags to remove.

replace

Named-list of tags to replce.

keep

List of tags to keep unchanged.

keep_private_tags

Keep private tags from DICOM instance.

keep_source

Keep original resource.

private_creator

Private creator to be used for private tags in replace.

force

Force tags to be changed.

dicom_version

Version of the DICOM standard to use for anonymization.

---

Method modify()

Modify an Instance

Usage

Instance$modify(
  remove = list(),
  replace = list(),
  keep = list(),
  remove_private_tags = FALSE,
  keep_source = TRUE,
  private_creator = NULL,
  force = FALSE
)

Arguments

remove

List of tags to remove.

replace

Named-list of tags to replce.

keep

List of tags to keep unchanged.

remove_private_tags

Remove private tags from DICOM instance.

keep_source

Keep original resource.

private_creator

Private creator to be used for private tags in replace.

force

Force tags to be changed.

---

Method get_nifti_file_content()

Get bytes of NIfTI file content.

Usage

Instance$get_nifti_file_content(compress = TRUE)

Arguments

compress

Compress to gzip (nii.gz) Default is TRUE.

---

Method download_nifti()

Download instance as NIfTI.

Usage

Instance$download_nifti(path, compress = TRUE, stream = FALSE)

Arguments

path

Path on disk.

compress

Compress to gzip (nii.gz) Default is TRUE.

stream

Should the resource be streamed and written to disk in chunks? Default is FALSE, which means the resource file contents are retrieved in their entirety and written to disk all at once.

---

Method download_image()

Download instance as an image.

Usage

Instance$download_image(
  path,
  frame = 0L,
  format = c("png", "jpeg"),
  render = TRUE,
  params = NULL,
  ...
)

Arguments

path

Path on disk.

frame

Index of the frame (starts at 0L). Default is 0L.

format

One of "png" or "jpeg". Default is "png".

render

Should the image be scaled (with RescaleSlope and RescaleIntercept) and windowed (with WindowCenter and WindowWidth, if available). Default is TRUE.

params

Optional named-list of query parameters.

...

Optional arguments passed on to png::writePNG() or jpeg::writeJPEG().

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Instance$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.