diff --git a/_posts/2021-12-01-dicom-file-format-basics.md b/_posts/2021-12-01-dicom-file-format-basics.md deleted file mode 100644 index 5856b63..0000000 --- a/_posts/2021-12-01-dicom-file-format-basics.md +++ /dev/null @@ -1,496 +0,0 @@ ---- -title: "DICOM File Format Basics" -page_title: "DICOM File Format Basics" -excerpt: "Explore the fundamentals of the DICOM file format! This quick -introduction covers the basics of DICOM's structure, its essential uses, and -tips for easily navigating its complex and abstract components." -date: December 1, 2021 -toc: true -toc_label: "Content" -toc_sticky: true -last_modified_at: December 1, 2021 -og_image: /assets/images/posts/dicom-basics/dicom-basics-header.jpg ---- - -{% include image.html - src="/assets/images/posts/dicom-basics/dicom-basics-header.jpg" - alt="dicom-basics-header" - caption="Image Source" -%} - -I would like to thank my former colleagues for introducing me to the DICOM world. -It's been a pleasure working with them and tackling many problems that come up -when one tries to understand all ins and outs of such a complex standard as DICOM. - -> **Disclaimer**: Everything presented here is part of public knowledge and can -be found in the resource section. - -In this post I'll try to present the basics of DICOM in plain language and -provide resources that helped me along the way. The DICOM Standard can be -overwhelming at first but with a nice introduction and basics the learning curve -can be flattened, which is my goal. - -I personally know that this post will be of interest to certain people and I'd -like to encourage them to contribute and share their knowledge. - -## Introduction - -For some odd reason you stumbled upon the DICOM Standard. Maybe at work, in a -conversation or somewhere else but you decided to google it and found out that -it means: Digital Imaging and Communications in Medicine. - -On Wikipedia page you've read: - -> Digital Imaging and Communications in Medicine (DICOM) is the standard for -the communication and management of medical imaging information and related -data. DICOM is most commonly used for storing and transmitting medical images -enabling the integration of medical imaging devices such as scanners, servers, -workstations, printers, network hardware, and picture archiving and -communication systems (PACS) from multiple manufacturers. - -And of course: - -> The standard includes a file format definition and a network communications -protocol that uses TCP/IP to communicate between systems. - -Now you have a pretty good idea that the DICOM Standard defines communication -protocol between different medical imaging devices and a file format. - -But how is it structured and how it works? -Since DICOM is enormous, where should you start? - -In my opinion, the best starting point is to understand the file format and how -it is used to represent medical images among other things. So, let's look at -some basic building block of DICOM file format. - -## DICOM file format - -DICOM file can be used to represent many things: Single/Multi frame Images, -Structured Reports, Encapsulated PDF storage, Videos etc. - -For now we will focus only on images. - -To open DICOM files you can use: [MicroDicom](https://www.microdicom.com/){:target="_blank"}, -it's a free DICOM viewer for Windows or if you prefer online viewer with -some sample files see: [DICOM Library](https://www.dicomlibrary.com/){:target="_blank"}. - -When you open a file you'll see something like this: - - -{% include image.html - src="/assets/images/posts/dicom-basics/microdicom-preview.jpg" - alt="microdicom-preview" - caption="MicroDicom Preview Source" -%} - -At the most basic level you can look at a DICOM file as a file that contains an -image and information about the image: how, when, and where it's been created, -who it belongs to, device used for its creation etc, and of course the image -itself. However, just like any other file format (PDF, Excel, Word ...) it has a -complex internal structure used for storing that information. - -### Structure - -DICOM file is comprised of a Header and a Data Set: - -{% include image.html - src="/assets/images/posts/dicom-basics/dicom-file-structure.png" - alt="dicom-file-structure" - caption="DICOM File Structure Source" -%} - -- Header, also known as DICOM File Meta Information, includes a preamble, -followed by 128 byte File Preamble, followed by 4 byte DICOM prefix, followed -by the File Meta Elements which include elements such as the TransferSyntaxUID -(which is very important for understanding the file format). - -- Data Set is a collection of Data Elements. - - -### DICOM Element - -If you look closely at the [MicroDicom preview image](#microdicom-preview) -from above, you'll see a list on the right hand side. -That list shows DICOM attributes. - -DICOM attribute (or Data Element) is a unit for storing information and it has -a well predefined tag and purpose defined in the DICOM Standard (we will see -later different types of tags that are not defined). For example the list can -contain the following attributes: - -Tag | Tag Description | Value | ------------ | --------------------- | ------------------------- | -(0002,0010) | Transfer Syntax UID | 1.2.840.10008.1.2.4.91 | -(0008,0008) | Image Type | ORIGINAL, PRIMARY | -(0008,0016) | SOP Class UID | 1.2.840.10008.5.1.4.1.1.2 | -(0008,0060) | Modality | CT | -(0010,0010) | Patient's Name | VladSiv | -(0010,0020) | Patient's ID | 0123456789 | -(0028,0100) | Bits Allocated | 16 | -(0028,0101) | Bits Stored | 12 | -... | ... | ... | ------------ | --------------------- | ------------------------- | - -> If you are interested, you can explore more attributes by browsing: -[Registry of DICOM Data Elements](https://dicom.nema.org/medical/Dicom/current/output/chtml/part06/chapter_6.html){:target="_blank"} - -Attributes are composed of, at least, three fields: - -- **Tag** - identifies the element -- **Value Length** (VL) - defines the length of the attribute's value -- **Value Field** (VF) - contains the attribute's data - -And for some types of Transfer Syntaxes (we will see later what they are), there -is another field: - -- **Value Representation** (VR) - describes the data type and format of the -attribute's value - -Visually we can represent that as: - -{% include image.html - src="/assets/images/posts/dicom-basics/dicom-element.svg" - alt="dicom-element" - caption="DICOM Element Source" -%} - -#### Tags - -Every DICOM element has a Tag that uniquely indetifies the element and is -represented as: `(gggg,eeee)`, where `gggg` represents the Group Number and -`eeee` the Element Number. - -Group and Element numbers are 16-bit unsigned integers and are represented in -hexadecimal notation. - -A Group is a collection of elements that are somehow related, -for example: - -| Tag | Tag Description | -| ------------- | --------------------- | -| (0010,0010) | Patient's Name | -| (0010,0020) | Patient ID | -| (0010,0021) | Issuer of Patient ID | -| (0010,0022) | Type of Patient ID | -| (0010,0030) | Patient's Birth Date | -| (0010,0040) | Patient's Sex | -| ... | ... | -| ------------- | --------------------- | - - -> Actually, a Group belongs to an attribute of an abstract concept called -**Information Object Definition** (IOD) and the Patient group to -Patient **Module** - I'll explain how it works later. - -#### Value Length - -Depending on VR, VL can be of defined or undefined lenght. If it's defined then -it's a 16 or 32-bit unsigned integer containing the explicit length of the -Value Field as the number of bytes that make up the Value. - -#### Value Field - -Represents an even number of bytes containing the Value of the Data Element. -It's obvious that the data type of the stored Value depends on VR as explained -above. - -However, VF can contain multiple values and that's defined by -**Value Multiplicity** (VM). For data elements that are defined in the Standard, each -element has a defined VM and if it is greater than 1, multiple values are delimited -within the VF. - -> To see VMs of tags defined in the DICOM Standard, please see: -[Registry of DICOM Data Elements](https://dicom.nema.org/medical/Dicom/current/output/chtml/part06/chapter_6.html){:target="_blank"} - -#### Value Representation - -VR is really important as it defines how the VF will be interpreted. The most -important thing to remember is that VR can be: - -- Explicit - Is contained in Data Element -- Implicit - Is missing from Data Element - -You may be asking now, if it's missing how do we know how to interpret the VF? - -Well, it's defined in the Standard, and when you get the Tag `(gggg,eeee)` you -know what to expect, that's why it's implicit. If something is not right, and -for example your application cannot parse the data element, then the data -element is not encoded in accordance with the Standard. - -If it's present in the data element. It contains two byte characters which are -always encoded using upper case letters. - -The list of possible VRs is quite extensive and details about encoding, character -repertoire, and length of value can be found in the Standard: -[Value Representation](https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2){:target="_blank"} - -To mention some of them: - -| VR | Name | -| ----- | ----------------- | -| CS | Code String | -| DS | Decimal String | -| DT | Date Time | -| LO | Long String | -| LT | Long Text | -| OB | Other Byte | -| PN | Person Name | -| SH | Short String | -| SQ | Sequence of Items | -| ... | ... | -| ----- | ----------------- | - -#### Public and Private - -The DICOM Standard allows private data elements which don't belong to Standard -Data Elements i.e. are not defined in the Standard. This allows different -implementations of communication of information. For example, private elements -can be used by different machine manufacturers to specify element where the -proprietary data is stored. - -However, private data elements have to have the same structure as Standard -Data Elements i.e. Tag, VL, VF, VR, VM etc. - -How do we distinguish between private and public elements? - -It's easy, public elements have an even Group number, while private groups -have odd numbers. - -> Note: Elements with Tags `(0001,xxxx)`, `(0003,xxxx)`, `(0005,xxxx)`, -`(0007,xxxx)`, and `(FFFF,xxxx)` cannot be used. To learn more about -implemention of private tags please see: [Private Data Element Tags](https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_7.8.1){:target="_blank"} - -#### Type of elements - -DICOM attributes may be required in a Data Set (depending on IOD or a SOP -class, we will define them later). - -Some of the attributes are mandatory, others are mandatory under certain -conditions and of course, some are completely optional. - -There are 5 types: - -- **Type 1**: Required data element, it cannot be empty. Absence of a value of -a Type 1 data element is a protocol violation -- **Type 1C**: Same as Type 1 but is required under certain conditions -- **Type 2**: Required data element, but it can be empty if the value is -unknown. For example, think of the Patient's name, it is a required element but the -actual name i.e. value can be unknown at the moment of performing a scan. -- **Type 2C**: Same as Type 2 but is required under certain conditions -- **Type 3**: Optional tags - -#### Nested Tags - -You can define nested tags in a DICOM Data Set, this is done using **Sequence -of Items** (SQ) VR as mentioned above. This allows you to define a tag that -has a sequence of items, where each item contains a set of Data Elements. - -For example, tag: `(0010,1002)` - _Other Patient IDs Sequence_; can contain many -items that represent Patient ID Data Set. If you are familiar with JSON -objects, you can look at it like: - -```json -{ - "Other Patient IDs Sequence": [ - { - "PatientID": "id", - "Issuer of Patient ID": "issuer", - "Type of Patient ID": "type", - "Issuer Of Patient ID Qualifiers Sequence": { - "Universal Entity ID": "uni", - "Universal Entity ID Type": "uni_type", - ... - } - }, - {...}, - {...} - ] -} -``` - -To be more precise about the structure of these items and nested data set, we -could depict it: - -{% include image.html - src="/assets/images/posts/dicom-basics/dicom-basics-sq.jpg" - alt="dicom-sq" - caption="Sequence structure, Source" -%} - -If you would like to know more about encoding of nested data sets, please see: -[Nesting of Data Sets](https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_7.5){:target="_blank"} - -### Transfer Syntax - -We now know that we can have different types of tags and value representations, -also that they can be implicit or explicit. When dealing with objects in general -we have to store them somehow and send them to different applications. Basically, -everyone should know how to read and use the object. To put it more precisely, -everyone should be able to serialize and deserialize a DICOM object. - -Transfer Syntax does exactly that, it tells you how to read a DICOM object. It -defines three things: - -- Explicit/Implicit VR - If VRs are present in a Data Element or not -- Big/Little Endian - Byte ordering, see: [Endianness](https://en.wikipedia.org/wiki/Endianness){:target="_blank"} -- Native/Encapsulated Pixel Data - If pixel data is compressed and what -compression algorithm is used - -However, the Transfer Syntax applies only to the Data Set part of a DICOM file, -while the File Meta Information has always the same encoding. To -quote the DICOM Standard: - -> Except for the 128 byte preamble and the 4 byte prefix, the File Meta -Information shall be encoded using the Explicit VR Little Endian Transfer -Syntax as defined in DICOM PS3.5. The Unknown (UN) Value Representation shall -not be used in the File Meta Information. -Ref: [DICOM File Meta Information](https://dicom.nema.org/medical/dicom/current/output/html/part10.html#sect_7.1){:target="_blank"} - -So, to read a DICOM file, you have to: - -- Skip preamble (Why? See: [Preamble Hack](#preamble-hack)) -- Confirm that it's indeed a DICOM file, by reading bytes 128-131 which should -be "DICM" i.e. DICOM prefix (don't rely on extenstions, it could be anything and -is not specified in the Standard) -- Start parsing all `0002` tags with Explicit VR Little Endian -- Get `(0002,0010)` - TransferSyntaxUID and use it to parse the Data Set - -Transfer Syntaxes are defines with UIDs: - -| Transfer Syntax Name | Transfer Syntax UID | -| ----------------------------------------------------------------------------------------------------- | ----------------------------- | -| Implicit VR Endian: Default
Transfer Syntax for DICOM | 1.2.840.10008.1.2 | -| Explicit VR Little Endian | 1.2.840.10008.1.2.1 | -| Deflated Explicit VR Little Endian | 1.2.840.10008.1.2.1.99 | -| JPEG Baseline (Process 1):
Default Transfer Syntax for Lossy JPEG
8-bit Image Compression | 1.2.840.10008.1.2.4.50 | -| JPEG-LS Lossless Image Compression | 1.2.840.10008.1.2.4.80 | -| ... | ... | - -To get the full list of available Transfer Syntax UIDs, please see: -[Registry of DICOM Unique Identifiers](https://dicom.nema.org/medical/dicom/current/output/chtml/part06/chapter_A.html){:target="_blank"} - -### SOP Class - -When it comes to information objects in the DICOM Standard, there is a lot of -abstract definitions, and I just mentioned some of them like _Information -Object Definition_ (IOD) and _Module_. - -These topic go beyond the basics of the file format but I'll try to give you -some really rough guidelines on how it works. - -If you are familiar with _Object Oriented Programming_ (OOP) you already know -that we try to model information in object-oriented abstract data models that -are used to specify information about the real world objects. In DICOM this -class is represented as IOD. We can use this class as a template and -instantiate it with attributes and that gives us a particular Data Set. - -Attributes of an IOD describe a property of a real world object and are -grouped into _Information Entities_ or _Modules_, depending if IOD is -_Normalized_ or _Composite_. - -If you are new to DICOM Standard, you may be asking: What in hell are you -talking about? -And I get your point, I like thinking about abstract concepts -but to really grasp them, they need to be introduced in an undestandable way -that showcases a real world application. - -If you open: [Dicom Standard Browser](https://dicom.innolitics.com/ciods){:target="_blank"}. -You'll see a list of Composite IODs (CIOD), and there are many of them, such as: -CR Image, CT Image, MR Image, US Image, Encapsulated PDF, etc. When you open -one of them you'll see Modules, which can be _Mandatory_ (M) or _User Optional_ -(U). These CIOD actually represent a template which is instantiated from an -abstact class, which we mentioned. - -All DICOM objects have to include a SOP Common Module, likewise if DICOM -object represents an image, it should include an Image Module. Other main modules -are: Patient, Study and Series. Additionally, there are specific modules, if -we define a DICOM object as a CR Image, we must include a CR Image Module and so on... - -**Service-Object Pair Class** (SOP Class) - contains the rules and semantics -that may restrict the use of the service in the **DICOM Message Service Element** -(DIMSE) Service Group and/or the attributes of the IOD. This basically means that -by defining a SOP Class of a DICOM object it specifies the mandatory and -optional modules of an IOD. - -> DIMSE is connected to the part of DICOM Standard that deals with the protocol. -This is not in the scope of this basic introduction, but if you are interested -check out: [Dicom Part 7 - Message Exchange](https://dicom.nema.org/medical/dicom/current/output/html/part07.html){:target="_blank"} - -SOP Class is defined by SOPClassUID and is always present in a DICOM file in the -(0008,0016) Data Element. Let's look at some examples: - -| SOP name | SOPClassUID | -| ----------------------------------------- | --------------------------------- | -| CR Image Storage | 1.2.840.10008.5.1.4.1.1.1 | -| CT Image Storage | 1.2.840.10008.5.1.4.1.1.2 | -| NM Image Storage | 1.2.840.10008.5.1.4.1.1.20 | -| MR Image Storage | 1.2.840.10008.5.1.4.1.1.4 | -| Encapsulated PDF Storage | 1.2.840.10008.5.1.4.1.1.104.1 | -| Ultrasound Image Storage | 1.2.840.10008.5.1.4.1.1.6.1 | -| Video Photographic Image Storage | 1.2.840.10008.5.1.4.1.1.77.1.4.1 | -| ... | ... | - -If you are interested in more SOP Class UIDs, please see: -[Registry of DICOM Unique Identifiers](https://dicom.nema.org/medical/dicom/current/output/chtml/part06/chapter_A.html){:target="_blank"} - -Now that we understand the SOP Class, it's important to understand that when -we create a DICOM file, this file is an instance of the SOP Class. That's why -we have a Data Element: **SOPInstanceUID** which is globally unique in a DICOM -file. - -Of course, there are other instances, for example: **StudyInstanceUID** - -uniquely identifies a study, which can contain many series that are identified -using **SeriesInstanceUID** and so on... - -### Preamble Hack - -In 2019, a new hack surfaced and it used DICOM files to enable malware to -infect patient data. It used the Preamble to insert itself into DICOM files and -exploit flaws in the design of DICOM. - -We know that the Preamble is a part of the Header and that it represents a 128-byte -section. The purpose of this section is to allow applications to use it for -specific implementations. For example, it could be used to contain information -enabling a multi-media applications to randomly access images stored in a DICOM -Data Set or any other specific implementation. - -The important thing here is that the DICOM Standard does not require any -structure and does not impose any requirements on the data inserted into the -Preamble. Basically we can insert whatever we want. This allows hackers to -masquerade an executable file as a DICOM image which will trigger an execution -of the malware. - -If you'd like to find out more about this hack, please read: -[HIPAA-Protected Malware? Exploiting DICOM Flaw to Embed Malware in CT/MRI Imagery](https://researchcylera.wpcomstaging.com/2019/04/16/pe-dicom-medical-malware/){:target="_blank"} - -## Final Words - -If you are just starting out with the DICOM Standard it can be daunting when -you look at the -[DICOM Standard](https://www.dicomstandard.org/current){:target="_blank"}, -22 parts where, for example, part 3 has 1802 pages in PDF format. -Just skimming through the whole Standard can take a while :D - -The aim of this article is to introduce the basic concepts, related to the -file format, in a clear and concise manner. Grasping the basics -will give you a good starting point for exploring the whole Standard. - -I hope that this article gets you interested in the DICOM world and -encourages you to dive deeper and research referenced material. - -If you have any questions or suggestions, please reach out, I'm always -available. - -## Resources - -- [DICOM Standard](https://www.dicomstandard.org/current){:target="_blank"} - Online DICOM -Standard, Current Edition -- [DICOM Standard Browser](https://dicom.innolitics.com/ciods){:target="_blank"} - Standalone -website that offers quick and really pleasent overview of DICOM attributes -- [DICOM is Easy](https://dicomiseasy.blogspot.com/){:target="_blank"} - Great blog about -sofware programming for medical applications -- DICOM sample files: - - [RuboMedical](https://www.rubomedical.com/dicom_files/){:target="_blank"} - - [Osirix Dicom Viewer](https://www.osirix-viewer.com/resources/dicom-image-library/){:target="_blank"} diff --git a/_posts/2022-01-01-dicom-file-processing.md b/_posts/2022-01-01-dicom-file-processing.md deleted file mode 100644 index e7291c8..0000000 --- a/_posts/2022-01-01-dicom-file-processing.md +++ /dev/null @@ -1,769 +0,0 @@ ---- -title: "DICOM File Processing" -page_title: "DICOM File Processing" -excerpt: "Discover how to handle and process DICOM files. Explore popular free -and open-source libraries that can help you develop applications for efficient -DICOM processing. These tools and libraries make managing medical images much -easier and straightforward." -date: January 1, 2022 -toc: true -toc_label: "Content" -toc_sticky: true -last_modified_at: January 1, 2022 -og_image: /assets/images/posts/dicom-playground/dicom-playground.jpg ---- - -{% include image.html - src="/assets/images/posts/dicom-playground/dicom-playground.jpg" - alt="dicom-basics-header" - caption="Image Source" -%} - -We'll explore some open source libraries in different programming languages and -how you can use them to process DICOM files. We'll cover the basics of removing, -modifying, adding data elements, changing compression, creating DICOM -files for testing, and masking parts of images for de-identification purposes. - -If you are new to the DICOM Standard and you are not sure how the DICOM file -format works, please read -[DICOM Basics]({% post_url 2021-12-01-dicom-file-format-basics %}) first. - -> **Disclaimer**: Everything presented here is part of public knowledge and can -be found in referenced material. - -## Open Source Libraries - -The following are some of the popular open source libraries for processing DICOM -files: - -- [PixelMed](https://www.pixelmed.com/){:target="_blank"} - Java DICOM Toolkit -which is a stand-alone DICOM toolkit that implements code for -reading and creating DICOM data, DICOM network and file support, support for -display of images, reports, and much much more -- [pydicom](https://github.com/pydicom/pydicom){:target="_blank"} - Pure Python -package for working with DICOM files. It lets you read, modify and write -DICOM data in an easy "pythonic" way. -- [Grassroots DICOM (GDCM)](https://sourceforge.net/projects/gdcm/){:target="_blank"} - -Cross-platform library written in C++ for DICOM medical files. It is -automatically wrapped to Python/C#/Java and PHP which allows you to use the -language you are familiar with and to integrate it with other applications. -- [dicomParser](https://github.com/cornerstonejs/dicomParser){:target="_blank"} - -Lightweight library for parsing DICOM in modern HTML5 based web browsers. -dicomParser is fast, easy to use and has no required external dependencies. -- [DCMTK](https://dicom.offis.de/dcmtk.php.en){:target="_blank"} - is a -collection of libraries and applications implementing large parts the DICOM -standard. It includes software for examining, constructing and converting -DICOM image files, handling offline media, sending and receiving images over -a network connection, as well as demonstrative image storage and worklist -servers. DCMTK is written in a mixture of ANSI C and C++. - -The choice depends on your use case and, of course, on the language you are -comfortable with. - -These libraries implement most of the things from the DICOM Standard and there -is no way I can cover all of them in this article. Therefore, we will focus only -on the PixelMed, pydicom, some of GDCM tools, and switch between them to implement -different functionalities. - -## Setup - -### PixelMed - -PixelMed is written in Java, so you'll need Java 1.8 or higher. After you -install Java, go to [PixelMed Directory Tree](https://www.dclunie.com/pixelmed/software/index.html){:target="_blank"}, -select the current edition, and download the `pixelmed.jar` (or use Maven/Gradle -if you are familiar with them). - -If you are not sure how to use this jar, I suggest you download -[Eclipse IDE](https://www.eclipse.org/downloads/){:target="_blank"}, -create a Java project and add `pixelmed.jar` to the project, see: -[How to import a jar in Eclipse](https://stackoverflow.com/questions/3280353/how-to-import-a-jar-in-eclipse){:target="_blank"}. - -PixelMed's API documentation can be found at [PixelMed JavaDocs](https://www.dclunie.com/pixelmed/software/javadoc/index.html){:target="_blank"}. - -### GDCM - -Source code: [Grassroots DICOM](https://sourceforge.net/projects/gdcm/){:target="_blank"}. - -There are premade tools which you can use: -- **gdcmdump** - dumps a DICOM file, it will display the structure and values -contained in the specified DICOM file. -- **gdcmanon** - tool to anonymize a DICOM file. -- **gdcmdiff** - dumps differences of two DICOM files -- **gdcmconv** - tool to convert DICOM to DICOM etc - -To use them you can either compile the source or download the binaries from -[GDCM Releases](https://github.com/malaterre/GDCM/releases){:target="_blank"}. - -> If you are on Linux, you'll have to add the gdcm `lib` folder to -`/etc/ld.so.conf` file or create new `.conf` in folder `.d`. Then -run `sudo ldconfig`. In order to have gdcm applications available in the -terminal as commands you'll have to add `bin` to `$PATH` -(globally or in `~/.bash_profile`). - -### pydicom - -This library requires python >= 3.6.1. I suggest you set up a virtual -environment where you can install packages using a dependency manager ([poetry](https://python-poetry.org/){:target="_blank"}, -[pipenv](https://pipenv.pypa.io/en/latest/){:target="_blank"}, -or any other). - -To get familiar with the library, please see: -[pydicom documentation](https://pydicom.github.io/pydicom/stable/){:target="_blank"}. - -## DICOM - -### Exploring Structure - -#### GDCM - -To explore the structure of a DICOM file, we can use `gdcmdump`: - -```bash -gdcmdump -``` - -This will give us an output like: - - - -```text -# Dicom-File-Format - -# Dicom-Meta-Information-Header -# Used TransferSyntax: -(0002,0000) UL 194 # 4,1 File Meta Information Group Length -(0002,0001) OB 00\01 # 2,1 File Meta Information Version -(0002,0002) UI [1.2.840.10008.5.1.4.1.1.12.2] # 28,1 Media Storage SOP Class UID -(0002,0003) UI [1.3.6.1.4.1.5962.1.1.0.0.0.1168612284.20369.0.3] # 48,1 Media Storage SOP Instance UID -(0002,0010) UI [1.2.840.10008.1.2.1] # 20,1 Transfer Syntax UID -(0002,0012) UI [1.3.6.1.4.1.5962.2] # 18,1 Implementation Class UID -(0002,0013) SH [DCTOOL100 ] # 10,1 Implementation Version Name -(0002,0016) AE [CLUNIE1 ] # 8,1 Source Application Entity Title - -# Dicom-Data-Set -# Used TransferSyntax: 1.2.840.10008.1.2.1 -(0008,0005) CS [ISO_IR 100] # 10,1-n Specific Character Set -(0008,0008) CS [ORIGINAL\PRIMARY\SINGLE PLANE ] # 30,2-n Image Type -(0008,0012) DA [20070112] # 8,1 Instance Creation Date -(0008,0013) TM [093126] # 6,1 Instance Creation Time -(0008,0014) UI [1.3.6.1.4.1.5962.3] # 18,1 Instance Creator UID -(0008,0016) UI [1.2.840.10008.5.1.4.1.1.12.2] # 28,1 SOP Class UID -(0008,0018) UI [1.3.6.1.4.1.5962.1.1.0.0.0.1168612284.20369.0.3] # 48,1 SOP Instance UID -... -``` - -This tool offers a quick and easy way to explore DICOM files and debug -applications that process DICOM files. - -Looking at the output we can see the _Dicom-Meta-Information-Header_ and -_Dicom-Data-Set_. Additionally, for each Data Element, we have a Tag -`(gggg,eeee)` then a VR, followed by a Value, and the information after `#` -represents: VL, VM, and Tag Name. - -`gdcmdump` comes with a lot of options that you can use to generate an output, -for more information please see: [gdcmdump](http://gdcm.sourceforge.net/html/gdcmdump.html){:target="_blank"} - -#### PixelMed - -The `AttributeList` class is a class in the PixelMed that maintains a list of -individual DICOM attributes. It could be used to get the structure of a file, -modify it, and save it. - -Using `.read(java.lang.String name)` we can read the tags: - -```java -package pixelmed_demo; - -import java.io.IOException; -import com.pixelmed.dicom.AttributeList; -import com.pixelmed.dicom.DicomException; - -public class demo_main { - - public static void main(String[] args) { - String filepath = args[0]; - AttributeList attList = new AttributeList(); - try { - attList.read(filepath); - System.out.println(attList.toString()); - } catch (IOException | DicomException e) { - System.out.println("Oops! Error: " + e.getMessage()); - } - } -} -``` - -Passing the same DICOM file we used in `gdcmdump` example as an argument, -we get: - -``` -(0x0002,0x0000) FileMetaInformationGroupLength VR=