Edit detail for Release_1.1.8 revision 1 of 1

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Editor: damberger Time: 2004/12/10 17:01:12 GMT+0
Note:

changed:
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This release makes additional improvements to spectrum and peak formats.

- New EASY spectrum format export feature accessible from the Tools menu of the CARA Explorer or the Spectrum menu of MonoScope. Use it to save all spectrum formats supported by CARA to EASY format. I don't create submatrices (since this is an outdated feature), instead there is only one single submatrix incorporating the whole spectrum. You can use this feature to create EASY from *.nmr files for backward compatibility with programs restricted to single spectrum format (e.g. DYANA, RADAR, etc.).

- Poly/HomoScope:

- Export Peaklist now also sets the color code of the peaks according to the link code.

- New Options "Use Link Color Codes" for Plane and Strips independantly

- New Menu "Set Link Params" for Plane and Strips, shortcut PA and ZPA

- Spin views now support peak colors corresponding to the Code filed of the Link alias

- Console/Batch-Mode: major exceptions are now caught without a dialog box. The name of the dumped repository is written to the command line (together with the error message). Pleas note that on Windows you need to add "-log <filename>" to the command line since console output is swallowed.

Intermediate release 1.1.8.1 (Nov. 20, 04):

- I refactored parts of the spectrum engine to allow only a subset of the spectrum resolution to be read from the hard drive. This feature is controlled by the actual screen resolution and size of the scope.

- As a result of this change a buffer corresponding to the size of the scope is allocated in memory (instead of the full size of the spectrum plane). I did this because more and more people are using really big spectra with really big planes. On some machines the allocation of large memory chunks leads to strange behaviour (non-reproducible crashes, etc.). With this change these memory problems should nolonger occur since CARA doesn't load the whole plane into memory any longer for doing a scale reduction.

- In contrast to XEASY, which only looks at a subset of the samples of the plane, CARA still looks at all available samples, accumulating them into a single value by maximum intensity. Consequently you still see all features of the spectrum without arbitrary details getting lost because of "brute force scale reduction".

- I also redesigned the loading procedure of Mono-, Homo-, Synchro- and PolyScope to load faster and smoother (featuring the correct scale reduction right from the beginning).

- CARA/Lua: new optional parameters nx and ny in Spectrum:getPlaneRange and nx in Spectrum:getSliceRange. If not set, all available samples of the plane/slice are used. Otherwise the parameters can be used to set the maximum number of samples to be fetched for a plane/slice (doing the scale reduction described above).

Intermediate release 1.1.8.2 (Nov. 24, 04):

- I implemented a simple BMRB parser able to read a reasonable subset of the BMRB star file format. The file must contain two _loop sections, one for the sequence (number, short name) and one for the atoms (number, residue, label, shift, etc.). I will provide an example later.

- You can now create a new project by importing a BMRB file (of the mentioned simple format). Use the item "Import from BMRB file..." from the context menu on "Projects" category or menu "Projects/Import".

Intermediate release 1.1.8.3 (Dec. 5, 04):

- Due to many requests I added the ZG command to NEASY. But keep in mind that I want people to use the CARA features and NEASY is only provided for backward compatibility (e.g. to view old projects etc.).

- Some optimizations in repository loading when spectra cannot be found, and with the file format filter in the open dialog box.

- I fixed a buffer overflow causing mysterious crashes (found due to hints by Veniamin).

- MonoScope: can now properly display the slices along all the dimensions of a 4D spectrum.

- MonoScope: contour threshold can now also be set for spectra which are not part of the repository.

- I also fixed a problem with byte order of NMR pipe spectra which caused the spectrum to have zero dimensions.

Cheers

Rochus

This release makes additional improvements to spectrum and peak formats.

New EASY spectrum format export feature accessible from the Tools menu of the CARA Explorer or the Spectrum menu of MonoScope. Use it to save all spectrum formats supported by CARA to EASY format. I don't create submatrices (since this is an outdated feature), instead there is only one single submatrix incorporating the whole spectrum. You can use this feature to create EASY from *.nmr files for backward compatibility with programs restricted to single spectrum format (e.g. DYANA, RADAR, etc.).
Poly/HomoScope:
- Export Peaklist now also sets the color code of the peaks according to the link code.
- New Options "Use Link Color Codes" for Plane and Strips independantly
- New Menu "Set Link Params" for Plane and Strips, shortcut PA and ZPA
- Spin views now support peak colors corresponding to the Code filed of the Link alias
Console/Batch-Mode: major exceptions are now caught without a dialog box. The name of the dumped repository is written to the command line (together with the error message). Pleas note that on Windows you need to add "-log " to the command line since console output is swallowed.

Intermediate release 1.1.8.1 (Nov. 20, 04):

I refactored parts of the spectrum engine to allow only a subset of the spectrum resolution to be read from the hard drive. This feature is controlled by the actual screen resolution and size of the scope.
As a result of this change a buffer corresponding to the size of the scope is allocated in memory (instead of the full size of the spectrum plane). I did this because more and more people are using really big spectra with really big planes. On some machines the allocation of large memory chunks leads to strange behaviour (non-reproducible crashes, etc.). With this change these memory problems should nolonger occur since CARA doesn't load the whole plane into memory any longer for doing a scale reduction.
In contrast to XEASY, which only looks at a subset of the samples of the plane, CARA still looks at all available samples, accumulating them into a single value by maximum intensity. Consequently you still see all features of the spectrum without arbitrary details getting lost because of "brute force scale reduction".
I also redesigned the loading procedure of Mono-, Homo-, Synchro- and PolyScope to load faster and smoother (featuring the correct scale reduction right from the beginning).
CARA/Lua: new optional parameters nx and ny in Spectrum:getPlaneRange and nx in Spectrum:getSliceRange. If not set, all available samples of the plane/slice are used. Otherwise the parameters can be used to set the maximum number of samples to be fetched for a plane/slice (doing the scale reduction described above).

Intermediate release 1.1.8.2 (Nov. 24, 04):

I implemented a simple BMRB parser able to read a reasonable subset of the BMRB star file format. The file must contain two _loop sections, one for the sequence (number, short name) and one for the atoms (number, residue, label, shift, etc.). I will provide an example later.
You can now create a new project by importing a BMRB file (of the mentioned simple format). Use the item "Import from BMRB file..." from the context menu on "Projects" category or menu "Projects/Import".

Intermediate release 1.1.8.3 (Dec. 5, 04):

Due to many requests I added the ZG command to NEASY. But keep in mind that I want people to use the CARA features and NEASY is only provided for backward compatibility (e.g. to view old projects etc.).
Some optimizations in repository loading when spectra cannot be found, and with the file format filter in the open dialog box.
I fixed a buffer overflow causing mysterious crashes (found due to hints by Veniamin).
MonoScope: can now properly display the slices along all the dimensions of a 4D spectrum.
MonoScope: contour threshold can now also be set for spectra which are not part of the repository.
I also fixed a problem with byte order of NMR pipe spectra which caused the spectrum to have zero dimensions.

Cheers

Rochus