I'm currently an MS student in Medical Physics and I have a great need to be able to overlay an isodose distribution from an RTDOSE file onto a CT image from a .dcm file set.
I've managed to extract the image and the dose pixel arrays myself using pydicom and dicom_numpy, but the two arrays are not the same size! So, if I overlay the two together, the dose will not be in the correct position based on what the Elekta Gamma Plan software exported it as.
I've played around with dicompyler and 3DSlicer and they obviously are able to do this even though the arrays are not the same size. However, I think I cannot export the numerical data when using these softwares.I can only scroll through and view it as an image. How can I overlay the RTDOSE to an CT image?
Thank you
for what you want it sounds like you should use Simple ITK (or equivalent - my experience is with sitk) to do the dicom handling, not pydicom.
Dicom has built in a complete system for 3D point and location specifications for all the pixel data in patient coordinates. This uses a bunch of attributes in the dicom files in the Image Plane Module set of tags. See here for a good overview.
The simple ITK library fully understands and uses the full 3D Image Plane tags to identify and locate any images in patient coordinates by default - irrespective of such things as the specific pixel spacing, slice thickness etc etc.
So - in your case - if you use SITK to open your studies, then you should be able to overlay them correctly "out of the box", because SITK will do all the work to parse the Image Plane Module tags and locate the data in patient coordinates - just like you get with 3DSlicer.
Pydicom, in contrast, doesn't itself try to use any of that information at all. It only gives you the raw pixel arrays (for images).
Note I use both pydicom and SITK. This isn't something bad about pydicom, but more a question of right tool for the job. In fact, for many (most?) things I use pydicom, but for any true 3D type work, SITK is the easier toolkit to use.
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I am working with a part that was taken from a *.acs point cloud map to a meshed part through Autodesk ReCap. This object had hidden features that I was unable to erase (or see) when converting from a *.acs (point cloud), to a *.rcp (ReCap file) to a *.obj (mesh), and I have not found an intuitive way to remove the "flash" from the sides without creating holes that I have not been able to fill. I tried manually removing these edges in MeshMixer and Meshlab, but feel like there must be an easier way than what I have tried so far. Image for reference
Thanks!
I'm trying to find the best strategy to align a SCNScene to a physical table. Just like the ARKit app WWWFreeRivers.
Currently I'm just testing out to map a simple plane model, with the same dimensions as the table. If I draw out the plane that ARKit detects, I can see that the plane is not very accurate with the edges. They always go outside of the edges (image below).
So I can't really rely on that plane, to just place the model in the center of this. The model is not rotated correctly either (image below).
I had another idea to use the ARReferenceImage technique, to take a picture of the table top texture, and let ARKit find and match this "image" of the table. But even with wood grain texture, it wasn't enough data for ARKit to recognize it. And ARKit just fails if you have these errors. It doesn't even try to do a bad match.
How can I go about doing this?
Ideas I've had so far:
Take image of table and use ARImageReference feature to match it. This didn't work. Maybe if I add some more interesting feature points to the table, like some sort of QR codes in the corners.
Detect the plane, and then tap the four corners on the table to map out a square, and use this.
Do as the WWW app, just place the object randomly on the plane, and then let the user scale, move and rotate the model to give it correct placement.
Any more ideas? What do you think will be the best approach to this?
Two options I can think of you could use.
You could create an ARWorldMap (iOS12+ only) and use it instead of the ARImageReference, walk around the area while creating a map that subsequent ARKit Sessions will remember. You can experiment slightly as to how to fit your models within the four corners of the table (this is slightly tedious w/o much help from the SceneView editor). However, when you load the saved ARWorldMap and localized against it (just like the ARImageReference), your model should fit within the four corners of the table every time.
If you use something like Unity (and its ARKit plugin), it has much more powerful Editor tools (3D viewer/designer). There are some tools that can help you save the map just like ARWorldMap but then bring in details of the map into the editor so you can line things up right really easily. Placenote's Spatial Capture toolkit can help here. Placenote (iOS11+) creates its own "World Map" but it exposes the visual details in the Unity editor, making it easier to line things up and then localize against (Example). The map is also stored on a managed cloud from the get-go to make sharing across phones much easier.
P.S: Both these options require you to keep the environment generally static (not large lighting changes etc.), though this was a similar constraint to when using ARIMageReference.
I'm trying to extract some a data (a map image) from a PNG file which is tiled somehow. The file itself is only 256x256 pixels (according to 'get info' on the mac) but is is 23MB. It is from an iPad app called Mud Map and it contains a map that I purchased but I've lost the original that I converted to this format. When I view this file (renamed to a .PNG) I see one section of the map - 256x256px.
I'm asking this question on StackOverflow because I want to know more about these tiled images. How does one create a tiled PNG and what is the software that will open and or create these things. I'm interested in what metadata is required too. I'm loving the outdoors and mapping!!
The answer to this question, is that it cannot be done in manner I have described.
The images in the PNG are not tiled, the the files are just merged together which is no doubt an individual feature of the program as is it does not appear to be any kind of standard.
I have no access to application you mentioned in IPad. Just share some thought about possible situation here.
1) Map tiles are commonly used in GIS web application such as Google maps and so on. It is used to improve the performance especially when user pan very often. A map displayed typical map window is divided into for instance 4*4 separate calls. So maybe only 4 call will be made when user just pan a little bit instead of get the whole map for the 16 tiles.
The source image for this tiles can be in pre-generated tiles or just one static map.
2) Assemble separate images to one in GIS is called image mosaic function. GIS server can read a collection of images and mosaiced them into one with the overlapping part handle based on a certain rule. And the images are in pre defined grid format which are seamless and no overlapping, then it is called tiled images. We could pre-generated the tiles from one mosaiced image, or we can server it on the fly. Some GIS server/library/application does have the tile server function built in.
I am using MYSQL workbench to generate an EER diagram, and to the best of my knowledge, one can not control the dimensions of the canvas, only the size in number of pages. This has the result that you get a huge amount of white space around your diagram, making it nearly unusable. Why anyone would design it this way is beyond me. There are a lot of questions which ask how to crop a pdf, but they are either more complicated (ie. crop to a certain dimension, or crop and output to different format and ratio) or they do not preserve the image quality, or they just plain do not work. My question therefore is this:
How does one create or convert an EER diagram using MySQL Workbench such that there are no white borders AND the image quality is preserved?
Note I asked the question here as it pertains to databasing, but apologies if it is in the wrong place.
Looks like what you are after is a way to limit the output of an image export to a relatively small area, so that it fits nicely in another document. Several options are possible:
1) Export as png and simply cut off the unwanted parts. Depending on the further usage this might be good enough.
2) Export as SVG and use any of the SVG editors to limit the image size to the wanted area only. Then convert it to the format you need in your target document.
3) Set a paper size in the model that encompasses the content as close as possible. E.g. the statement paper type is quite small. Then rearrange your objects. Resize them if you need larger ones. By setting a larger font (via Preferences) you should be able to make the entire appearence larger. Then export as PDF.
I see some ways to do it:
1) Draw using OpenGL programmatically.
2) Draw using QuartzCore and CoreAnimation programmatically.
3) Draw map in AutoCad and then somehow connect it to iOS.
4) Draw map using SVG.
Requirments are supporting pathfinding and gps navigation.
For first 2 ways I think that it's expensive in terms of performance way, redraw all elements on scaling; and I don't think that this way may have GPS-navigation support.
Using AutoCad pictured maps is hard to understand for me how to connect it with graphs\paths for pathfinding.
My colleagues will develop this app on web using SVG. I found it - https://github.com/SVGKit/SVGKit , but still have no idea how it will support pathfinding and navigation.
I would appreciate any help.
Generally there are two types of map application:
A) They display a map, (with or without a user position) without needing to calculate a path like a navigation system does (see point B)
B) Application that use the vectors of a map and calculate something: e.g to find a best path. The shortest connection, e.g A navighation system , etc.
Application for A) are usually less complex then that of B), because the vectors can be somewhat inacurate, have no conections, have small gaps, have no logic between the edges, etc.
1) To only display a building map, you would only need a list of edges. (An edge is pair of coordinates (x1,y1) - (x2,y2). How ever you get that. E.g MapInfo Professional format mif/mid.
Or even you could dispaly a pdf that contains the map of the builing. Right with the built in PDF View, (also with SVG but more difficult).
Things get much more complicated if it is not a relative map, but also a map that is positioned with an reference coordinate system, like latitude/longitude (WGS84).
In that case you would use a Tool (mapInfoProfessional, to import AutoCad DXF Files, and apply 3 GPS measured reference points at the corner of the house, and convert that to LatLong WGS84 coordinates system.
With ios you cannot measure that 3 Points because you cannot average a position, ios stops sending when you are standing still at one corner of the house.
You could try to extract the positions from a google earth satellite foto if you are living in a region where google Sattelite fotos have high resolution. (But this might violate the license conditions of that Satellite Foto provider (Topic: derived data))
Finally you now have a list of edges in Lat Lon coordinate System.
For Displaying I personally would either do with 1) OpenGL) or 2) Quartz2D.
Now the Path finding part.
Probaly you need a second "map" that defines the possible paths inside the building.
This structure must be a connect graph (points with connected neighbours).
Computer games do it that way. (Some even allow you to display that path in developper mode)
The path can be drawn, in a different layer of the floor plan. But this path
has higher requirements: No gaps are allowed, all must be perfect connected.
Call that layer "Path" and export it as own plan.
Now use only this path layer, and import, and create a graph of nodes with connect neighbours.
Use Dijkstra Algo to search for shortest path.