IT-LIST Digest 12Topics covered in this issue include:  1) Tif-2-Cif?	by sshaib@lsumc.edu (Shaibani, Sanan)  2) ImageTool Version 1.2	by Peter Stalmans   3) ImageTool Version 1.2	by Peter Stalmans   4) Re: Tif-2-Cif?	by "S. Brent Dove"   5) Re: result difficult export	by "S. Brent Dove"   6) New ImageTool Version 1.2	by "S. Brent Dove"   7) Server Problems	by "S. Brent Dove"   8) Re: Problems locating source code	by "S. Brent Dove"   9) what is cif	by sshaib@lsumc.edu (Shaibani, Sanan) 10) Problems unzipping idsdk.zip	by "Michael Moed" ----------------------------------------------------------------------Date: Fri, 1 Mar 96 12:16:09 -0600From: sshaib@lsumc.edu (Shaibani, Sanan)To: it-list@sparky.uthscsa.eduSubject: Tif-2-Cif?Message-ID: <9603011816.AA08329@unixsrv1.lsumc.edu>>> Does any one know how I can convert a TIF or BMP file to CIF.>>I hvae not heard of a 'CIF' type. You may mean 'GIF'. If so, then >LVIEW or PaintShop will do the conversion. Open the file and 'save as' >the other format. PaintShopPro will also do this in batch mode, I >believe. >>Christopher Spry>I also thought it was GIF but on the file type I am looking for is CIF.  Itis used in the micro-electronic industry. Does any one know how to convert to CIF or SIF format?  *************************************************************Sanan Shaibani                    sshaib@lsumc.edu______________________________________________________________LSU eye center                    phone:  504-568-6700 ext 4372020 gravier str. ste. B.         fax  :  504-568-4210New Orlean, LA 70112-2234______________________________________________________________------------------------------Date: Mon, 04 Mar 1996 12:35:21 +0100From: Peter Stalmans To: it-list@sparky.uthscsa.eduSubject: ImageTool Version 1.2Message-ID: <2.2.32.19960304113521.00681d80@popserv.kuleuven.ac.be>This weekend I've installed version 1.2 on our computer system (Win95), andI'm impressed with all new features in the newest release. The binary importfilter is much improved, and the easy interaction with the result windows isan enormous improvement.Congratulation to all contributors!I have one remark though: when I quit ImageTool, I always get an errormessage as follows: This program  has caused an illegal operation and willbe shut down. (I've enclosed details as an attachment).This seems not to be machine-dependent, since it appeared both on a 486 andPentium machine.I also have two suggestions for further development:1) Regarding the import filter: most imaging systems I'm aware of that usetheir own binary file format, use a header in the file (that can be skippedusing the current import filter) where the exact width and height of thepicture are stored (usually in 2-byte format, sometimes byte-swapped).Usually, the header also contains a byte that specifies the number ofpictures in the file, as well as the bits-per color.If the import filter could be manually instructed to read these bytes anduse them accordingly, importing binary image would even more simple.2) Regarding the area and line drawing: it would be interesting if the areaor line-of-interest could be saved, and re-loaded. This could have followinguse: in microscopy, data are often compared before and after a certainevent, so a series of images is obtained.If it could be possible to load the first image, then to draw the necessaryareas or lines of interest, and save them, one could load the next image(s),and reload the exact same areas or lines of interest, to obtain measurementsfrom the exact same place in the whole series of images.Greetings,Peter Stalmans, MDPeter.Stalmans@med.kuleuven.ac.beLaboratory of Physiology KULeuvenHerestraat 49B-3000 LeuvenBelgiumtel: +32-16-34 71 46fax: +32-16-34 59 91------------------------------Date: Mon, 04 Mar 1996 12:36:02 +0100From: Peter Stalmans To: it-list@sparky.uthscsa.eduSubject: ImageTool Version 1.2Message-ID: <2.2.32.19960304113602.0068b7b8@popserv.kuleuven.ac.be>--=====================_825935762==_Content-Type: text/plain; charset="us-ascii"This weekend I've installed version 1.2 on our computer system (Win95), andI'm impressed with all new features in the newest release. The binary importfilter is much improved, and the easy interaction with the result windows isan enormous improvement.Congratulation to all contributors!I have one remark though: when I quit ImageTool, I always get an errormessage as follows: This program  has caused an illegal operation and willbe shut down. (I've enclosed details as an attachment).This seems not to be machine-dependent, since it appeared both on a 486 andPentium machine.I also have two suggestions for further development:1) Regarding the import filter: most imaging systems I'm aware of that usetheir own binary file format, use a header in the file (that can be skippedusing the current import filter) where the exact width and height of thepicture are stored (usually in 2-byte format, sometimes byte-swapped).Usually, the header also contains a byte that specifies the number ofpictures in the file, as well as the bits-per color.If the import filter could be manually instructed to read these bytes anduse them accordingly, importing binary image would even more simple.2) Regarding the area and line drawing: it would be interesting if the areaor line-of-interest could be saved, and re-loaded. This could have followinguse: in microscopy, data are often compared before and after a certainevent, so a series of images is obtained.If it could be possible to load the first image, then to draw the necessaryareas or lines of interest, and save them, one could load the next image(s),and reload the exact same areas or lines of interest, to obtain measurementsfrom the exact same place in the whole series of images.Greetings,Peter Stalmans, MD--=====================_825935762==_Content-Type: application/mac-binhex40; name="ITError.txt"Content-Disposition: attachment; filename="ITError.txt"--=====================_825935762==_Content-Type: text/plain; charset="us-ascii"Peter.Stalmans@med.kuleuven.ac.beLaboratory of Physiology KULeuvenHerestraat 49B-3000 LeuvenBelgiumtel: +32-16-34 71 46fax: +32-16-34 59 91--=====================_825935762==_--------------------------------Date: Mon, 04 Mar 1996 08:04:59 -0600 (CST)From: "S. Brent Dove" To: IT List Subject: Re: Tif-2-Cif?Message-ID: <01I1XMFH1EQM0092W3@uthscsa.edu>Recently on the ITList>Does any one know how I can convert a TIF or BMP file to CIF.>Any info on Tif-2-Cif type files or macros would be very helpful.I am unaware of such a format as CIF.  Please explain what is the real name for the format, what is it used for and what type of software uses this format.ThanksS. Brent Dove                            Voice: (210) 567-3333Diagnostic Sciences                      Fax:   (210) 567-3334University of Texas                      Email: dove@uthscsa.eduHealth Science Center                    Web:   ddsdx.uthscsa.eduSan Antonio, TX    USA                   ftp:   maxrad6.uthscsa.edu------------------------------Date: Mon, 04 Mar 1996 08:05:02 -0600 (CST)From: "S. Brent Dove" To: IT List Subject: Re: result difficult exportMessage-ID: <01I1XMFJBNRM0092W3@uthscsa.edu>Recently on the ITList>There is difficult to export the result, apparently there is no carriage>return at the end of each data line.>>All results are copied in one long line on the first row, into a spreadsheet.>>Could you make the modification to this remark?With the introduction of version 1.2 and the new improved spreadsheet this has been addressed. We have tested the output of the save and print cammands.  You can also copy and paste directly into Excel for more sophisticated data analysis.S. Brent Dove                            Voice: (210) 567-3333Diagnostic Sciences                      Fax:   (210) 567-3334University of Texas                      Email: dove@uthscsa.eduHealth Science Center                    Web:   ddsdx.uthscsa.eduSan Antonio, TX    USA                   ftp:   maxrad6.uthscsa.edu------------------------------Date: Mon, 04 Mar 1996 08:05:06 -0600 (CST)From: "S. Brent Dove" To: IT List Subject: New ImageTool Version 1.2Message-ID: <01I1XMFLGTJQ0092W3@uthscsa.edu>Hello ImageTool Users,First, I would like to thank all of you for your support in the development of ImageTool.  Especially those who have helped with suggestions and bug reports.Second,  I would like to announce the release of Version 1.2.The new version is presently being distributed by either the Web site or the ftp site.Version 1.2 has several major improvements.  With this version we have increased the capabilities of IT to handle 8, 10, 12, 14, and 16 bit gray scale data.  This will allow ImageTool to be used on almost all medical imaging modalities.  This includes CT, MRI, PET, SPECT, Ultrasound and many other modalities.  All the analysis anad measurments work on the "real" data.  We have also provided a mechanism for Window and Level for display on 8 bit systems.  We are working on a DICOM plugin which will support the DICOM 3.0 file format. This should be completed soon.  This feature is also important for the use of the high bit depth scanners that are available for scanning radiographs and autoradiographs used in molecular biology.With the release of version 1.2, UTHSCSA ImageTool now provides support for multiple imagedata sets called Stacks. Image Stacks provide a mechanism for relating images in either time or space. Temporally-related images can be used to produce cine motion of real events or animation of graphical data. Image frames can be played back at 1 to 30 frames per second depending upon hardware. Sequences can be played in forward or reverse. Spatially-related images, such as Computed Tomography, Magnetic Resonance Imaging or Confocal Microscopy can be displayed as a stack. Images can be stepped through one at a time or played as a cine loop. These stacks can also be used as three dimensional data structures forextracting and rendering 3D objects. Check out our Shocking demonstration of Image Stacks at our WWW site utilizing the new Netscape Navigator 2.0 and MacroMedia SchockWave technology.UTHSCSA ImageTool version 1.2 now has a new and improved spreadsheet for the results ofyour analysis. Using FarPoint Technologies 32 bit Spread/DLL, ImageTool provides a better view of your data. Results are automatically updated to the spreadsheet window. The built in spreadsheet automatically calculates the mean and standard deviation of all columns in real time. The spreadsheet can have up to 2 billion by 2 billion cells. Data from the ImageTool spreadsheet can be save as tab deliminated text files or copy and pasted directly into Microsoft Excel.This version addresses all bugs reported as of 2/20/96.  We hope that you will find this upgrade a significant improvement to ImageTool.  Well, that's three releases in six months, I keep telling myself we'll get some sleep tommorrow.Well so long for now and Happy Leap Year.S. Brent Dove                            Voice: (210) 567-3333Diagnostic Sciences                      Fax:   (210) 567-3334University of Texas                      Email: dove@uthscsa.eduHealth Science Center                    Web:   ddsdx.uthscsa.eduSan Antonio, TX    USA                   ftp:   maxrad6.uthscsa.edu------------------------------Date: Mon, 04 Mar 1996 08:05:20 -0600 (CST)From: "S. Brent Dove" To: IT List Subject: Server ProblemsMessage-ID: <01I1XMFWLMK80092W3@uthscsa.edu>Hello IT users,We have had several complaints about accessing the ftp server.  We are running a Pentium processor with 32 MB of RAM and Window NT ftp server from Microsoft. I am not sure what these problems are or what they are caused by.  If anybody has any suggestions please let me know. We are presently trying to get several mirror sites to ease this problems  I will inform the group as soon as these are available.  Again we are sorry for any of the problems. We will keep trying to eliminate this.S. Brent Dove                            Voice: (210) 567-3333Diagnostic Sciences                      Fax:   (210) 567-3334University of Texas                      Email: dove@uthscsa.eduHealth Science Center                    Web:   ddsdx.uthscsa.eduSan Antonio, TX    USA                   ftp:   maxrad6.uthscsa.edu------------------------------Date: Mon, 04 Mar 1996 08:05:29 -0600 (CST)From: "S. Brent Dove" To: IT List Subject: Re: Problems locating source codeMessage-ID: <01I1XMG2QXDK0092W3@uthscsa.edu>Recently on the ITList some of you have commented on the lack of source code.> I have been unable to find the source code for Image Tool.>     >     I attempted to access the source code from the following areas:>     >     ftp://maxrad6.uthscsa.edu/  - Unable to enter the pub directory.>     ftp://maxrad6.uthscsa.edu/ftp/pub/it/source - No source code found.>     >     I'd like to write some plug-ins, but need the source to do it.We have been working very hard to release the latest version of ImageTool 1.2.  We did not want people developing code for 1.1 which had some bugs and version 1.2 has some changes that would affect the development of plugins.  We removed the source code for this reason.  Version 1.2 is HERE!!! along with the ImageTool SDK.  We do not intend to remove this source code. Please feel free to download and develop plugins for IT.S. Brent Dove                            Voice: (210) 567-3333Diagnostic Sciences                      Fax:   (210) 567-3334University of Texas                      Email: dove@uthscsa.eduHealth Science Center                    Web:   ddsdx.uthscsa.eduSan Antonio, TX    USA                   ftp:   maxrad6.uthscsa.edu------------------------------Date: Mon, 4 Mar 96 10:56:44 -0600From: sshaib@lsumc.edu (Shaibani, Sanan)To: it-list@sparky.uthscsa.eduSubject: what is cifMessage-ID: <9603041656.AA28288@unixsrv1.lsumc.edu>>Recently on the ITList>>>Does any one know how I can convert a TIF or BMP file to CIF.>>Any info on Tif-2-Cif type files or macros would be very helpful.>>I am unaware of such a format as CIF.  Please explain what is the real >name for the format, what is it used for and what type of software uses >this format...real name: Caltech Intermediate Form (CIF),used in : Integrated circuit layout, software: Program like MAGIC.*************************************************************Sanan Shaibani                    sshaib@lsumc.edu______________________________________________________________LSU eye center                    phone:  504-568-6700 ext 4372020 gravier str. ste. B.         fax  :  504-568-4210New Orlean, LA 70112-2234______________________________________________________________------------------------------Date: Mon, 04 Mar 96 14:45:27 EDTFrom: "Michael Moed" To: IT-LIST@sparky.uthscsa.eduSubject: Problems unzipping idsdk.zipMessage-ID: <9602048259.AA825979645@winhitc.atlantaga.attgis.com>          I've downloaded the source code in file idsdk.zip for V1.2 of      ImageTool.  When I unzip the archive, I get a zip error that occurs on      file piprop~1.h.  It prohibits me from extracting this file, or any      subsequent files.  I've tried downloading to two different sites (home      and office), and get the same error.          Please help!          - Mike               ------------------------------End of IT-LIST Digest 12