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Dicom Operator - EsmeProcess

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3.5
3.5 | 6 ratings Rate this file 24 Downloads (last 30 days) File Size: 2.73 MB File ID: #43397 Version: 1.5
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Dicom Operator - EsmeProcess

by

Jun Li (view profile)

 

06 Sep 2013 (Updated )

EsmeProcess functions dicom image operation including viewing, drawing, writing and statistic.

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Description

EsmeProcess: The main program is functioning dicom operation with drawing/painting multiple Region Of Interest (ROI) on a given dicom image, saving/retrieving the results into/from the dicom header, computing various statistic required, and viewing 3D images. All the imroi tools (freehand, circle, rectangle, polygon) are used to define ROI region(s) with a sophisticated binary operation between them. The statistical functions include bar, plot and boxplot. Further functions are provided:
SAVE:
          - Save the ROI/painting into dicom header; save the image, statistic, mask and ROI in .dicom, .png, .mask and .xlsx formats correspondingly.
READ:
          - Read the ROI/painting from header and paint to the dicom image; also load.mask.
EXPANSION:
          - Expand the ROI based on the size defined in the option file.
APPLY_TO_OTHERS:
          - Apply the ROI to other images within the same dicom series either directly or by loading a .mask.
STATISTIC:
          - Calculate the mean, deviation and percentiles of aggregated ROI and display by plot, bar or boxplot in Statistic Menu. The aggregated ROI is computed based on an interactive binary operation. Each shape's histogram can be shown by right-click menu.
OPTIONS:
          - Load and configure the parameters. For example, the text object can be switched off by setting 'roitexton' parameter to zero in Options.
INFOEDITOR:
          - View, edit, anonymize and recover dicoms and headers
          - View cross-section of 3D Images by scrolling up/down mouse wheel

Generated Information:
                    - Binary mask (.mask).
                    - Region Of Interest (.xlsx).
                    - Statistic of ROI (.png).
                    - Dicom images with painting history (.dicom).

This program is also a good example for people who intend to use some undocumented tools such as uitree, recent files menu and listbox context menu etc.

Acknowledgements

Get Drives, Rapid Lossless Data Compression Of Numerical Or String Variables, Boxcount, Findjobj Find Java Handles Of Matlab Graphic Objects, Ini Config, Lacunarity Of A Binary Image, Interactive Dicom 3 D Viewer, Recursive Directory Listing Enhanced Rdir, Enhanced Dicom Viewer, and Subtightplot inspired this file.

Required Products Image Acquisition Toolbox
Image Processing Toolbox
MATLAB
MATLAB release MATLAB 8.0 (R2012b)
Other requirements Parallel Computing Toolbox (Optional) Need Excel supported
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Comments and Ratings (7)
23 Nov 2016 Wouter

Wouter (view profile)

Windows only now.

it would be very nice to replace all backslashes '\' with forward slashes, or even better, the filesep() function.

on top of that; please get rid of nargchk and replace it by narginchck and nargoutchk

01 Jun 2016 Michael Liu

Hi,

I am trying to use the script but I get this error and I don't know why.

Error using sprintf
Function is not defined for 'matlab.ui.Figure' inputs.

Error in CROIEditor/createwindow (line 14)
set(this.guifig, 'Tag', ['EsmeFigures', sprintf('%.f', this.guifig)]);

Error in CROIEditor (line 107)
this.createwindow;

Error in EsmeProcess (line 49)
CROIEditor(pathstr);

Comment only
13 May 2016 Daniel Bridges  
13 May 2016 Daniel Bridges

Extracting the zip and setting the path, the program hangs upon execution (following the Readme file): MATLAB R2016a reports "Busy" indefinitely after several warnings about deprecated NARGCHK, much longer than the readme file's stated "few seconds". Installing it through the Add-Ons menu, it opened after a few seconds (with the same warning, "NARGCHK will be removed in a future release. Use NARGINCHK or NARGOUTCHK instead.").

Thank you for the additional code to read; it appears to have many comments as well to guide comprehension.

13 May 2016 Daniel Bridges

The program hangs upon execution (following the Readme file): MATLAB R2016a reports "Busy" indefinitely after several warnings about deprecated NARGCHK, much longer than the readme file's stated "few seconds".

Nonetheless, thank you for the additional code to read; it appears to have many comments as well to guide comprehension.

14 Aug 2014 John Spartan

Hi!

It's a very useful script for my work. However I have a question about fractal abundance, what does that mean? I don't fully understand what's the concept behind this word...
Could you explain it to me please?

Thank you very much

13 Feb 2014 Jun Li

Jun Li (view profile)

 
Updates
13 Sep 2013 1.2

A text object and ui context menu are created from each corresponding shape. The text object can be switched off by setting 'roitexton' parameter to zero in Options. Ui context menu supports histogram etc for each individual shape.

06 Dec 2013 1.3

Add 3D cross-section image viewing to the InfoEditor

07 Jan 2014 1.4

1. Correct some minor errors.
2. Improve 3D viewer.
3. Include a Readme.txt for installation at root, and include a 1-3D fractal analysis directory with commands (will have further development).

07 Mar 2014 1.5

1. Correct some minor errors.
2. Set automatic windowing in the main figure, parameterized by windowxp and windowyp in config.ini
3. Create contrast slider and brightness slider in InfoEditor related to transverse etc. directions.

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