Low (Resolution) and Order (of applying transformations)

I'm doing a project that involves taking huge images of 400,000,000 pixels, 20000 X 20000, 700 MB on disk, scaling them down and cutting them into reasonably sized tiles (512x512 pixels).


In this post I want to present how simple code re factoring involving merely changing the order of applying the same transformations rewarded an enormous X20 performance gain.


As a first step, I had to order extra 8GB RAM for my workstation. Once thay have arrived (eBay, 100$, 1 week) I could finally click the input file and display it on windows image preview. Before that, my workstation, initially having only 2GB, hang for 20 minutes every time I accidentally hovered over the file.

The next step was to realize that .NET 2.0 bitmap classes won't do the trick. But than I was surprised to discover that WPF BitmapSource and its sub-classes (System.Windows.Media.Imaging) are capable of handling these very large images so I built the code around them avoiding a native C++ bite-cruncher completely. This was a very good start. It made me very happy.

The third step was to wrap the cropped images in DICOM. This is a subject for a dedicated, yet to come, post about the new multi-frame objects and concatenations. Then came the last two steps that proved out to be challenging.

My initial code looked like this:

1. Use ScaleTransform to down-scale the original image to the required resolution
2. Loop over the down-scaled image on X and Y to do the tiling (The Cut function)
3. Use CroppedBitmap to do the cropping (in the loop)

Here it is:

Documentation Update for version 2.0.1.9

The online documentation is now updated for version 2.0.1.9. In the new documentation there's new page with information for DICOM conformance that is useful for writing the DICOM Conformance Statement.

RZDCX 2.0.1.9

A new release of ZRDCX, 2.0.1.9, was released today. This release fixes the following issues:

#	Type	Status	Created	Changed	Version	Title
Description
291	code	fixed	Jan 30	Jan 30		DICOMDIR with strict = false fails on file names with .'s	edit
Create filenames like 1.2.3.4.dcm ScanAndCreate(..., false) -> Exception Reported by SBX
290	new	fixed	Jan 19	Jan 19	2.0.1.8	MoveAndStore - Single threaded C-MOVE duplexing control and data	edit
Add a method MoveAndStore to DCXREQ to allow one command that performs both the C-MOVE and the C-STORE commands on separate but semi-synced associations.
287	new	fixed	Dec 12	Dec 12	2.0.1.8	Minor logging additions to RZDCX	edit
Fix log messages when pres ctx id not found in store

Issue 291 addresses a very popular feature request to enable creation of DICOMDIR even when the filenames are not according to the standard. For example filenames with the instance uid like 1.2.3.4.5.6.dcm are not valid reference file id's according to the standard. Nevertheless, sometimes you would like to create a DICOMDIR file for other purposes other than exporting data on a CD. The ScanAndCreate method of DCXDICOMDIR takes a "strict" parameter that when set to false, will generate a DICOMDIR regardless of the validity of it's content (as long of course that the files are DICOM files).

Issue 290 is a new feature of RZDCX that enable to run a complete C-MOVE SCP with a single command including the incomming association. More about this feature in the upcoming chapter of the DICOM Tutorial.
Here's a short example

        public void MoveAndStore()

        {

            // Create an object with the query matching criteria (Identifier)

            DCXOBJ query = new DCXOBJ();

            DCXELM e = new DCXELM();

            e.Init((int)DICOM_TAGS_ENUM.patientName);

            e.Value = DOE^JOHN";

            query.insertElement(e);

            e.Init((int)DICOM_TAGS_ENUM.patientID);

            e.Value = @"123456789";

query.insertElement(e);

            // Create an accepter to handle the incomming association

DCXACC accepter = new DCXACC();

            accepter.StoreDirectory = @".\MoveAndStore";

Directory.CreateDirectory(accepter.StoreDirectory);

            // Create a requester and run the query

DCXREQ requester = new DCXREQ();

            requester.MoveAndStore(

                MyAETitle, // The AE title that issue the C-MOVE

                IS_AE,     // The PACS AE title

                IS_Host,   // The PACS IP address

                IS_port,   // The PACS listener port

                MyAETitle, // The AE title to send the

                query,     // The matching criteria

                104,       // The port to receive the results

                accepter); // The accepter to handle the results

        }

This single command takes care of all the details of a C-MOVE transaction. Instead of running an accepter on another thread to wait for the C-MOVE results, we pass the accepter as a parameter to the MoveAndStore method of the requester. Note that there's a new set property in DCXACC that enables setting the directory to store the incoming files. All the callbacks of DCXACC and DCXREQ can be used as well just as before.

Issue 287 is a small log enhancement that maxes it easier to to diagnose association problems. The log now shows very clearly when a presentation context for a command was not negotiated.

DICOM Query/Retrieve Part I

It all started when I was sitting in a cubicle with a customer, looking at the code of their workstation performing a Query/Retrieve cycle and though everything did look familiar and pretty much straight forward something bothered me.

Query/Retrieve, or Q/R for short, is the DICOM service for searching images on the PACS and getting a copy of them to the workstation where they can be displayed.

Q/R is a fundamental service and every workstation implements it. This sounds like a trivial task, just like downloading a zip file from a web site but there are a lot of details to take care of and while writing this post I realized that I will have to split it to a little sub-series. Today's post will be about the Query part and in the next post I'll get to the Retrieve.

To search the PACS we use the DICOM command C-FIND. This command takes as an argument a DICOM object that represent a query. The PACS transforms the object that we send to a query, probably to SQL, runs it and then transform every result record back into a DICOM object and send it back to us in a C-FIND response. The PACS sends one C-FIND response for every result record. While still running, the status field of the C-FIND response command is pending (0xFF00). The last response has a status success. It may of course fail and then RZDCX will throw an exception with the failure reason and status. It may also succeed but with no matches (empty results set).

Let's do some examples. This code constructs a query for searching patients:

            // Fill the query object

            DCXOBJ obj = new DCXOBJ();

            DCXELM  el = new DCXELM();

            el.Init((int)DICOM_TAGS_ENUM.QueryRetrieveLevel);

            el.Value = "PATIENT";

            obj.insertElement(el);

            el.Init(0x00100010);

            el.Value = "R*";

            obj.insertElement(el);

            el.Init(0x00100020);

            obj.insertElement(el);

            el.Init((int)DICOM_TAGS_ENUM.PatientsSex);

            obj.insertElement(el);

            el.Init((int)DICOM_TAGS_ENUM.PatientsBirthDate);

            obj.insertElement(el);

Introduction to DICOM - Chapter 6 - Transfer Syntax

Transfer syntax defines how DICOM objects are serialized. When holding an object in memory, the only thing that matters is that your application can use it. The internal representation of the object is your own business. However, when sharing objects with other applications, everyone should be able to use the same object. The common solution for such problems is serialization.

Serialization is the process of writing a data structure or object state to wire i.e in a format that can be stored in a file or memory buffer, or transmitted across a network so it can be read on the other side of the wire or later by the same or by another process.

There's no shared memory in DICOM but it can be easily made using the same mechanism that is utilized for networking and files alike i.e. serializing the object into memory according to the rules dictated by the standard i.e. using transfer syntax.

In this post I'll cover the following issues:

• Present the term Transfer Syntax, 
• Why Transfer Syntax is required 
• What is Transfer Syntax used for 
• How Transfer Syntax is set when using 
• DICOM files 
• DICOM network

So, as I said, the serialization in DICOM is governed by a term called Transfer Syntax.

Transfer Syntax is defined at the object level and is the syntax for serializing a DICOM object. We have seen transfer syntaxes already in chapter 5 when dealing with association negotiation but did not discuss them. In order for an application to read a DICOM object from a network wire, it has to know the rules that were used to write the object into the wire. In the association request the calling AE sends a list of abstract syntaxes with SOP Class UID's. For every SOP Class, the calling AE sends a list of transfer syntax UID's. In the association response the called AE selects one of the transfer syntax UID's for every SOP class it accepts.

Special offer for the new HL7Kit Pro 1.5

The new version 1.5 of HL7Kit Pro - HL7 to Database Integration Engine was released today. To celebrate the new release, the new version is offered at only $249 and includes all 4 applications in a single installation package. We've come to realize that our users prefer having the entire product installed on the production server including the HL7 Sender, HL7 Receiver and the HL7 Mapping Tool.

The main new feature of the new release is the support of multiple protocol versions and multiple mapping rules for a single runtime service. The runtime service can be configured to use different message definition files and different mapping XML for every remote application. This feature was requested long ago by many customers and a workaround to allow this was introduced in version 1.2. Now this feature is fully integrated into the product. The new release can be downloaded here.

HL7Kit Video Tutorials

If one picture worth a thousand words, how much does a 20 minutes video tutorials worth?
The HL7Kit web site promise that "You are 20 minutes away from HL7 integration!" I checked that again, this time on film.
From download to runtime deployment, a series of five detailed videos showing step by step how to set up a ADT^A01 message interface using HL7Kit.
Here it is. Comments and questions are most welcome.