NRecon version history Update guidelines: Before updating your NRecon/NReconServer, please backup your current version (NRecon.exe, NRecon.hlp, NReconServer.exe, NReconServer.hlp)! Updating is nothing else than copying the new files (the *.exe and *.hlp files) to their corresponding directory. For the distributed/cluster version, you do need to do it for all PC's and for both NRecon and NReconServer. ----------------------------------------------------------------------------------- Update history: --Version, 1.6.3.2, Aug 2010: ***Bug fixes: 1. Navigation image (projection) was not loaded properly for an incomplete oversize scan (e.g., 1 sub-scan out of a multi-part oversize scan; or a single scan with name convention of an oversize scan). --Version, 1.6.3.1, July 2010: ***Added or modified functionalities 1. Support now reconstruction for differential phase contrast imaging (irrelevant for CT users). 2. Bed-shift correction for rotating-gantry systems. 3. Change general image display mode (COLORONCOLOR -> HALFTONE): subtle differences in large zoom. 4. TView is removed from the toolbar. 5. CTvox has been added to the toolbar. 6. Support for datasets containing more than 10000 slices (4-digit file indices -> n-digit file indices, usually either 4 or 8). Support of n-digit indices by other SkyScan software will follow soon. ***Bug fixes: 1. Protocol files could not be read properly on Windows 7. --Version, 1.6.3.0, Apr. 2010: ***Added or modified functionalities 1. NRecon/NReconServer: automatic startup/shutdown the server PC's. To startup a server PC remotely, MAC address is required. See FAQ list for how to set it up. 2. In combination with InstaRecon 1.2.0.0: enable defect pixel correction; enable smoothing kernels. --Version, 1.6.2.0, Feb. 2010: ***Added or modified functionalities 1. NRecon, option "X/Y alignment with a reference scan": more flexibility and options are given for this option. 2. NRecon shortcut keys to start batch (CTRL ALT B), to start preview (CTRL ALT P), to start reconstruction (CTRL ALT S), to add current dataset to batch (CTRL ALT A). 3. NRecon (UI): similar to DataViewer, the profiling is now invoked by right-mouse click instead of left-click. 4. NRecon (UI): to invoke HU calibration, press Ctrl key and drag with right-mouse- button over an area. 5. NRecon, option "Show/Modify thermal shifts ...": this tool is revised and one can now modify the shifts manually and individually. 6. NRecon(UI): in case of dual monitors, the position of the window is remembered. ***Bug fixes: 1. NRecon, option "Adjust connections and then reconstruct an oversize scan": various bugs were found and fixed. The bugs include failures in matching, failures in writing results due to an improper range, distorted image (in case of interpolation using JPG format). 2. NReconServer (preview): in some extreme situations, the preview image was truncated. Fixed. 3. NReconServer: in accurate mode, a portion of the slices were missing if more than 4 threads are used. Fixed. --Version, 1.6.1.5, Oct. 2009: ***Bug fixes: 1. User interface (NRecon): window not properly refreshed or flickering when the main window is being resized. Fixed. 2. User interface (NRecon): in case of hot spots, the alignment images were not properly scaled, resulting in very dark images. Fixed. 3. User interface (NRecon): “No server available” appeared frequently when exchanging servers. Fixed. 4. Default rcp (reconstruction protocol file): it was not enabled correctly. 5. NRecon/Control software: when NRecon is on and a request to load a dataset from within a control software, it was not initialized properly. Fixed. ***Added or modified functionalities 1. NReconServer: in case of 180 scans, use as many projections as there exist. 2. NRecon, option "X/Y alignment with a reference scan": the region-of-comparison can now be defined as a rectangle instead of 2 lines. 3. NRecon, option "Adjust and reconstruct an oversize scan": a new option to recover an oversize scan in case of mismatch at one of the junctions. 4. NRecon/InstaRecon: no version control is applied to InstaRecon server, however, a warning is displayed in case of version mismatch. Reconstruction with step other than 1 is now enabled. 5. NRecon: "automatic naming" option in control software results in scan names containing "~0000~", which is a name convention for listmode scans. From now on, these scans (listmode name convention, but only one frame is available) are treated as a normal scan instead of a listmode scan. --Version 1.6.1.3, June 2009: ***Bug fixes: 1. Occasional crash of 64-bit NReconServer running on computers with large memory (>4GB). ***Added or modified functionalities 1. NReconServer runs now up to 8 threads instead of maximum 4 threads. Depending on the PC, speed increase of up to 150% has been observed by doubling the number of threads. --Version 1.6.1.2, June 2009: ***Bug fixes: 1. In version 1.6.1.1, NRecon crashes at exit (mainly on 32-bit PC's). This would also cause InstaReconServer to crash. --Version 1.6.1.1, June 2009: ***Bug fixes: 1. NReconserver crashed occassionally since version 1.6.0.3: bug is related to the introduction to JPG files with pixel size smaller than 389nm. 2. Bug in batch manager: if the "move up" or "remove" button is used while an oversize scan is involved, "loading failure" may occur afterwards. 3. NReconServer: when changing the number of threads, it was not recorded. Fixed. ***Minor modifications: 1. In preview, negative values may be truncated occasionally (can be seen on the histogram). This truncation is now removed. --Version 1.6.1.0, May 2009: ***Minor modifications: 1. Two additional smoothing kernels are introduced. 2. X/Y alignment with a reference scan: the projection pairs to compare are now based on available projections, not on expected projections from the reference scan. --Version 1.6.0.3, Apr. 20, 2009: ***New functionalities 1. It is now compatible with InstaRecon server. (See user manual for more information.) 2. Reconstruction for scans with a spiral orbit. 3. X/Y alignment with a reference scan. Specially useful for lengthy scans with high resolution. Actions->X/Y alignment with a reference scan. 4. Reconstruction speed up for data from BIOPTONICS scanners. 5. NReconServer: option to change the number of threads used for reconstruction. Standard: 2. Comments: Only ~10% speed increase going from 2-threads to 4-threads can be observed on platforms tested so far. 6. Option to schedule a batch job to start automatically at a given moment within 24 hours. Actions->Schedule batch job. ***Minor modifications: 1. UI: a small icon is displayed next to the server name. When the server is active, this icon represents the server program in use. This is important to avoid confusions for users with a licensed InstaRecon server program. 2. When loading a dataset with thermal-shift tags: the tags are first read to determine the range. This may take a while for large datasets: the progress info is displayed on the status bar below. 3. UI: more help information/hints are given on the status bar below. 4. NRecon: when starting up the first time, no batch manager and no preference dialog window will be shown. ***Bug fixes NRecon/NReconServer: 1. Local version: the server was started recursively. This caused dead-lock if the server couldn't be started. Fixed. 2. Output in JPG format: if the pixel size is less than 389nm, it was incorrectly written. To read these JPG files correctly, latest DataViewer (>1.4.1.0) and CTan (>1.9.2.3) are required. 3. NRecon, reconstruction protocol (rcp): the default RCP file name was not kept.. --Version 1.5.1.8, Mar. 13, 2009: Release for Bioptonics: ***Minor modifications (only for datasets from Bioptonics scanners): 1. Post-alignment: default to a step size of 0.5 (settings, fine-tuning). 2. Fine-tuning for defect-pixel masking --Version 1.5.1.5, May. 15, 2008: Intermediate update for minor changes on urgent user request. Other requests are not implemented yet but scheduled. Update both NRecon and NReconServer. ***Bug fixes NRecon/NReconServer: 1. Advanced engineering mode: projection rotation option produced inconsistent images between preview image and final reconstructed images. This was particularly the case when ring correction is used. 2. NReconServer 64-bit: incorrect available memory estimation in case more than 4 GB RAM is available. 3. NRecon (Aug. 18): NRecon would crash if it was started with a non-existing file. ***Minor modifications: 1. Image display: whenever no corresponding image is available, the projection image for navigation is displayed instead. ***Added or modified functionalities 1. Read-only input (such as a CD-rom, or any storage device with read-only attribute) is enabled. This is implemented as an option in the user preferences. One can choose where to put the output files and some temporary files among: 1. Data folder, this is default and will write any output in the input folder; 2. Sub folder, a sub-folder "reconstructed" under the input folder will be used; 3. Given folder, a sub-folder named after the dataset itself will be created under this given folder. Whenever the input folder is read-only, a given folder will be searched; if not defined, the user will be asked where to put the results. Please note: certain advanced functions will still require to write into input folder and sometimes even the input images ! 2. Keyboard shortcuts for preview (Ctrl+Alt+P), start reconstruction (Ctrl+Alt+P), start fine tuning (Ctrl+Alt+T), and send to batch (Ctrl+Alt+B). --Version 1.5.1.4, Feb. 25, 2008: Intermediate update for bug fixing. Update both NRecon and NReconServer. ***Bug fixes NRecon/NReconServer: 1. Inconsistent slice numbers if the reconstruction step is other than 1. The problem might occur in both cluster version and local version. With local version, the problem would only become obvious in case of connected scans. 2. Ring correction might be insufficient under special situation, e.g., when thermal shifts (a hidden parameter for users) are presented in acquired data. ***Minor modifications: 1. Recognize XRF data ***Added or modified functionalities 1. Read-only input (such as a CD-rom, or any storage device with read-only attribute) is enabled. This is implemented as an option in the user preferences. One can choose where to put the output files and some temporary files among: 1. Data folder, this is default and will write any output in the input folder; 2. Sub folder, a sub-folder "reconstructed" under the input folder will be used; 3. Given folder, a sub-folder named after the dataset itself will be created under this given folder. Whenever the input folder is read-only, a given folder will be searched; if not defined, the user will be asked where to put the results. Please note: certain advanced functions will still require to write into input folder and sometimes even the input images ! 2. Keyboard shortcuts for preview (Ctrl+Alt+P), start reconstruction (Ctrl+Alt+P), start fine tuning (Ctrl+Alt+T), and send to batch (Ctrl+Alt+B). --Version 1.5.1.3, Nov. 6, 2007: Intermediate update for bug fixing. Only NRecon in Cluster version needs to be updated. ***Bug fixes NRecon: 1. Cluster version only: due to a bug the connections might be broken during a batch. 2. Minor fix in the Advanced tab: information about defect pixels were not presented well. --Version 1.5.1.2, Nov. 22, 2007: Internal pre-release only. --Version 1.5.1.1, Nov. 6, 2007: Both NRecon and NReconServer should be updated. In preparing for 64-bit version, several functions (convolution, median filtering, JPG library) had to be replaced. This may introduce minor negligible differences due to rounding errors relative to previous versions. NReconServer is now provided in 64-bit. This version works together with 32-bit NRecon. No 64-bit NRecon is provided. ***Added or modified functionalities 1. Ring artifacts correction using defect pixel mask: a defect pixel on camera (abnormally high or low intensity) may cause severe rings. These pixels can now be detected (automatic or manual adjustment) and replaced by neighboring pixels. 2. Data consistency check: a new option in menu Actions for trouble shooting purpose. 3. An additional reconstruction mode is added as an option: more accurate but much slower (see Preferences page). 4. NRecon/NReconServer cluster: added option to allow user to view the speed record of each node, and alter it if necessary (see documentation for connection window). 5. NRecon/NReconServer cluster: increased stability in case of read/write failure due to the use of multiple nodes. 6. NRecon/NReconServer cluster: slightly improved job distribution (balance). 7. Undersampling option: variable undersampling factor (down to 250x250). The undersampling is now done at reconstruction level. 8. NRecon/NReconServer cluster: connection is automatically disconnected if the connection stays idle for a given amount of time.. 9. Recognize and enable reconstruction of a 4D scan (acquired with list-mode and sorted with Tsort). ***Subtle modifications: 1. Image range: by check on "positive values only" in the preferences, the lower range would be set at 0 at the first preview or whenever the auto button is clicked. 2. Histogram: double-click in the histogram window will switch on/off log scale of the vertical aixs. 3. Hounsfield unit: default HU calibration on 1076 scanner (control software) is recognized, if any. 4. External programs (CTan, DataViewer, TView) can be always started, even if there is no result to view. 5. Multiple entries of the same dataset in batch: it is now allowed (but use it with caution!). Any existing results will be warned and may be removed at the time of submission. Once batch processing starts, no files will be removed explicitly (overwriting can happen). 6. NReconServer_error.log is relocated: instead of using the directory where NReconServer is installed, this file is located now in the same system directory of NRecon if NRecon also runs on the computer, otherwise in C:\SkyScan\NRecon (automatically created if not exist). 7. User interface is slightly adapted: a new tab called "Advanced..." is added for a few parameters which are not frequently used. ***Bug fixes NRecon: 1. Post-alignment display: change of color scale was not remembered. 2. Post-alignment estimation: it would fail in case of small projection image, and/or larger image portion; wrong in case of big sample due to incorrect estimation of air intensity. 3. Very small discontinuity at optical axis in vertical direction (visible in saggital/coronal view for some objects): caused by incorrect interpolation. Fixed. 4. Navigation window: when type a slice number, image was not displayed automatically. 5. NRecon/NReconServer local: dead loop at start up if NReconServer could not be started normally. Fixed. --Version 1.5.0, Feb. 19, 2007: Intermediate release for optical scanners. Both NRecon and NReconServer should be updated. Major modification: added processing step to remove defect pixels (mask threshold) . --Version 1.4.4, July. 31, 2006: Both Nrecon and NReconServer should be updated. ***Bug fixes NRecon: 1. The "use 180+ only" flag was omitted when a job was sent to the batch manager. 2. The [bottom, top] range of an oversized scan might be altered when sent to the batch manager. 3. Job distribution might be unbalanced among nodes for an oversized scan. 4. Fine tuning for post-alignment: when the last reconstructed was with alignment 0, viewing was disabled. ***Bug fixes NReconServer: 1. A bug causes failure to do reconstruction (conv. failed). Problem occurred mainly for dataset with large cone angle (mostly, large dataset as well), when the smoothing option is used and when the [bottom, top] range is outside of the recommended area. 2. Minor changes to avoid read/write error/conflicts. This may cause slightly longer waiting time in case of I/O problems. ***Subtle modifications: 1. "Remove all" button on the batch manger window. 2. Title bar: remaining time in minutes is given. 3. NReconServer: dead-pixel mask is in use. The mask is created automatically by searching for pixels with zero value. This function is hidden from users and is always applied. --Version 1.4.3, Feb. 13, 2006: Both Nrecon and NReconServer should be updated. ***Bug fixes: 1. Small differences (in the order of 1/10000 ~ 1/1000) in images could be observed in some cases when repeating reconstruction with same parameters, for the same or different slice ranges --- a bug reported by a careful user: many thanks from the programmer. There were several causes for this bug: incorrect projection range for a partial cross-section range in certain combination of the parameters; slightly different interpolation method in two different reconstruction modes; a "randomness" mechanism in case of half-pixel post-alignment. This bug has been fixed and tested carefully. As a result of the bug fix, the preview is slightly slower than previous versions. 2. A bug in I/O when mapped network drive is used. More explanation can be found in the installation guide relating to I/O and shared directory. 3. Combination of undersampling and ring-artifacts correction did not work: this bug was introduced only since version 1.4.2 . 4. Bug reported and fixed on Jan. 23, 2006 (only NRecon is concerned). ROI used could be different than what the user defined. This would occur in limited situations: after loading parameters from a log file or from a predefined rcp file with ROI, and the reference length of the ROI was different from the projection width as shown on the "overview" page, and the ROI is situated towards the right/bottom edges. After this bug fix, the reference length of the ROI and the projection width as shown on the "overview" page should always be the same, no matter how and from where you retrieve the ROI definition. 5. Three options in the Preferences were ignored silently: "Default output file format: BMP", "Draw scales as default", "Def. cross-section rotation (in deg.)". Now they will be taken into account when "loading last-used parameters" becomes effective, i.e., when a dataset is not already in the batch list, and has never been reconstructed before and the option "Use last-used param. instead of default protocol" has been checked. Bug fixed on Jan. 30, 2006. 6. Reconstruction range in batch: if the range (top/bottom slices) was outside of the recommended range, it was automatically "shrunken" to within the recommended range. This undesired feature is removed now. Feb. 13, 2006. ***Subtle modifications: 1. To avoid overwriting, there is now an option to cancel reconstruction if previously reconstructed files are found ( Jan. 30, 2006). 2. Cluster version only: at start up, if there is no license found, a license.txt file (in the directory where NRecon is located) may be saved with the license ID for applying for license later ( Jan. 30, 2006). ***Added or modified functionalities 1. A non-standard option is added, upon request of some users: higher-order polynomial beam-hardening correction, known as "external beam hardening correction" for the ConeRec users. To avoid surprises, please read the document (FAQ list) about it carefully before switching this option on. 2. A non-standard 32-bit floating-point file format (F4F) is introduced. Again, to avoid surprises, you are kindly asked to read the document (FAQ list) first before switching it on. This file format is used as an additional output dataset, not as an alternative output: you will always get two output datasets if this option is turned on and this file format will consume 4 times disk space of that for a BMP dataset! The further support of this file format from SkyScan is very limited: only by DataViewer (from version 1.2.2 on). --Version 1.4.2, Dec. 12, 2005: Both Nrecon and NReconServer should be updated. ***Bug fixes: 1. Dataset with an odd projection width (e.g., 1241x1028 matrix which can be generated by 1172 scanners) could not be reconstructed. 2. During an oversized scan, the user interface was temporarily enabled between reconstructions of two sub-scans: this might cause unnecessary user interference to the reconstruction and might have the reconstruction process unexpectedly altered. 3. TIFF file format (output): the tags were not strictly in ascending order which is against the rule but would hardly cause any problem in most cases. (Some third-party software might require this rule to be respected. ) 4. ROI option in batch: due to a bug the ROI actually used was the last-used-ROI-for- the-given-matrixsize and could be completely different than what you meant. Now fixed. 5. The shadow image was put upside-down accidentally after a reconstruction with output format JPEG: only exist since version 1.4 and it did not have any consequence on your resulting images, unless you reconstruct the same dataset a second time immediately --- then the reference image (*_spr.bmp) might be upside-down. Now fixed. ***Added or modified functionalities 1. Ring artefact correction procedure to cope with our dual-camera 1178 model. Added functions for NRecon to work together with a control software (by the time of this update, only for 1178 model). 2. Added 8-bit TIFF as input (only for projection dataset --- potential format for 1178 model). 3. Slight improvement in image quality: occasionally it could be noticed that the left/right sides of a cross-section image were not symmetric (problem more pronounced in case of a combination of horizontal oversize and 180+ scans). This is now improved. ***Subtle modifications: 1. The display (Actions->Save as ...) can now also be saved in JPG format, using the compression factor as defined in Options->Preferences. 2. The log file: version number of NRecon is now in 3 digits, i.e., 1.4.2 instead of 1.4. 3. Parameter information is now recorded in NReconServer_error.log --- for debug purpose only. --Version 1.4.1, Nov. 21, 2005: Update due to a bug which changes the noise pattern in the resulting cross-sections: for both cluster version and local version. Both NRecon and NReconServer have to be updated. ***Bug fixes: 1. The filtering kernel was accidentally changed from Hamming window to RAMP filter in 1.4.0. This would cause more noisy image, therefore higher smoothing number would be necessary. The filter kernel is now switched back to Hamming window (default filtering for CT reconstruction). --Version 1.4, Nov. 1, 2005: No major improvement/change in image quality or reconstruction speed in this version. However, a few new functions will make it much easier to use. ***Added or modified functionalities 1. A free version of NRecon/NReconServer is now provided: the local NRecon/NReconServer, which is meant to replace ConeRec gradually. The local version has full functionality as the distributed/cluster version, but both NRecon and NReconServer have to run on one and the same computer. This version can be downloaded for free. 2. The distributed/cluster NRecon/NReconServer: the NRecon license can be installed for all users or only for the current user (relevant for multi-user environment only). No demo version is made available any more (the local version should be used for that purpose). A one-month evaluation license is available for free upon request. 3. The process of oversized scans has been completely reconsidered and redone: they can be now processed as if they are just one normal scan, with a few precautions. Required by several users, the post-alignment values can be adjusted per sub-scan. It is recommended to read the document to fully utilize the features for oversized scans. 4. Post-alignment correction. Improved accuracy in estimation. Profiling is enabled on the alignment image to help manual adjustment. The post-alignment option is now also available for in-vivo scanners (1076, 1078). See documentation for more details. 5. A "fine-tuning" function is provided to help users adjust parameters by a few trials: the post-alignment, the beam-hardening, the ring-correction level and the smoothing width. More details in the documentation. 6. Improved functionalities for saving/loading a reconstruction protocol file (*.rcp). Possibility to view/edit a protocol file is also provided. A default protocol file can be defined in the preferences. This feature will become important when NRecon is used together with a control program (not yet fully implemented in control programs). 7. Disk space check before starting a reconstruction/batch. 8. Added JPG format (8-bit): you may save the cross-sections directly in jpg format. It is recommended to use 100% compression factor in order to keep all the details. ***Bug fixes: 9. ROI is now forced to be within FOV. 10. Corrupted alignment image and failure during reconstruction: it was caused by datasets whose projection width is not a multiple of 4 (e.g., 1023 instead of 1024). 11. Occasionally corrupted scales information, wrong z value in oversized scans: now fixed/improved. 12. The progress window disappeared occasionally, which made cancelling a reconstruction in a decent way impossible. Fixed. 13. Negative time estimation: fixed. ***Subtle modifications: 14. Zooming function: the image will stay focused when you zoom in/out. 15. Title bar: progress information are put here. Dataset information are now to be found in the overview page. 16. For the *.spr image (the reference shadow image, used by DataViewer, CTan, TView, etc.), an option (set in preferences) is given to have inverted color scale with respect to the cross-section images. 17. Double-click anywhere on the projection image will move the preview slice (the green line) to that position. Also you may click on the number fastest on the reconstruction page to move the current preview slice to the fastest position. 18. Drag-and-drop a dataset to NRecon or start NRecon from a control program: no warning will be given if there is already a copy running. Instead, the running copy will be brought to the foreground and the given dataset will be loaded if the running copy was not busy. --Version 1.3 (Release version), March 31, 2005: ***Bug fixes: 1. Inconsistency between preview image and final reconstruction, when ring artifact correction is used. The inconsistency could be noticed as well at the edge slices of a volume reconstruction, when ring artefact correction is used. 2. No alignment image (display only) or wrong alignment image, but no influence on the reconstructed image. It occured for certain type of scanner types due to the internal thermal- shift correction(mainly on the Nano CT scanners). 3. Memory violation error from NReconServer, caused by incorrect estimation of memory requirement. It happened very rarely but rather consistently: increase the reconstruction range slice by slice to the point that the reconstruction mode is about to change (internal and automatic). 4. Problem could occur when both smoothing and under-sampling are used. ***Added or modified functionalities 5. Added functionality to allow profiling: use left mouse-button click, hold and drag. 6. Added icons on toolbar for zooming. 7. Added button on tool bar to allow user to go through projections/cross-section fast without starting up another program. 8. Added function to have 2 configurations (on connection window): local and network configuration. One can switch one configuration to another easily. Simplified network configuration set up window. 9. Square ROI -> rectangular ROI. By default, the ROI is assumed to be rectangular, but you may choose to force the ROI to be square as it was before. 10. Retrieve parameters created by ConeRec: the dynamic range is automatically adjusted. 11. Parameter retrieving at loading time: the previously used parameters (except post- alignment value) can be loaded automatically. You may switch it off in the Preferences if you do not like this feature. 12. Ring artefact correction level: increased from 10 to 20. The level remains absolute, i.e., 3 on a range of 0-10 is the same as 3 on a range of 0-20. 13. A few "permanent" windows could be closed/destroyed accidently by pressing Esc/Enter/Space key. This is now fixed. 14. Improved time estimation and job division based on automatic time recording. Reconstruction times are automatically recorded when no ROI is used (most reliable). 15. Last version aborts reconstruction when one of the servers fails. This version would continue as long as there is at least one server remains going. The "lost" work will be re- distributed later. --Version 1.2 (Beta version), Feb. 2005: