fxihub / hawk Goto Github PK

When playing around with the ring example, I noticed that the left image of the HawkGUI (set at real image as default) may freeze (reproducibility has to be checked) when the HDF5 files of the working directory are removed before the phasing is restarted. The old (removed) image is still loaded in memory on which operations can be performed (e.g. Fourier transform), but the image does not update when the program runs. This bug has not occurred to the right image so far.

It seems that the file watcher for the support at least keeps following the old directory.

Create a new option container called for example Initial support with all the options concerning it. Also implement bluring for creating the initial support from autocorrelation for the threshold algorithm (now only implemented for area algorithm)

Sometimes pieces of the plot are drawn outside its widget, even in other windows.

Title says it all

Sometimes when running in local mode the log plot stops being updated.
Unable to reproduce though.

Initial phases option should be named more generaly, like for example "Starting point", and given options like random_phases, zero_phases, random_object, flat_object. Then the random initial intensities option can be removed. The initial realspace image option should be left and always take precedence over the others.

Unsure if this is related to a bug in hawk or libspimage, but when using hawk_image_write() with the .cxi file format (that calls sp_image_write() that eventually calls write_cxi()) in the iteration loop of uwrapc.c, the output .cxi file is damaged and cannot be opened despite the program running without warnings. h5debug says:

HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
#000: H5F.c line 1534 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#1: H5F.c line 1325 in H5F_open(): unable to read superblock
major: File accessability
minor: Read failed
#2: H5Fsuper.c line 334 in H5F_super_read(): unable to find file signature
major: File accessability
minor: Not an HDF5 file
#3: H5Fsuper.c line 155 in H5F_locate_signature(): unable to find a valid file signature
major: Low-level I/O
minor: Unable to initialize object
cannot open file

This error does not occur when using sp_image_write() in image_to_png, where I debugged the current .cxi file I/O support, where the output h5debug reads:

Reading signature at address 0 (rel)
File Super Block...
File name (as opened): real_space-0000099-2.cxi
File name (after resolving symlinks): real_space-0000099-2.cxi
File access flags 0x00000000
File open reference count: 1
Address of super block: 0 (abs)
Size of userblock: 0 bytes
Superblock version number: 0
Free list version number: 0
Root group symbol table entry version number: 0
Shared header version number: 0
Size of file offsets (haddr_t type): 8 bytes
Size of file lengths (hsize_t type): 8 bytes
Symbol table leaf node 1/2 rank: 4
Symbol table internal node 1/2 rank: 16
File status flags: 0x00
Superblock extension address: UNDEF (rel)
Shared object header message table address: UNDEF (rel)
Shared object header message version number: 0
Number of shared object header message indexes: 0
Address of driver information block: UNDEF (rel)
Root group symbol table entry:
Name offset into private heap: 0
Object header address: 96
Cache info type: Symbol Table
Cached entry information:
B-tree address: 136
Heap address: 680

Has anyone managed to write .cxi file format with uwrapc? Any help to solve this problem is appreciated..

It would be nice to have Hawk tunnel automatically through 1 firewall when using RPC with ssh.

The title says everything.

The link should be
https://github.com/FXIhub/libspimage.git

NOT
https://github.com/filipemaia/hawk.git

Otherwise it will crash after the sort.

Currently this seems to make HawkGUI crash with std:alloc error.

LC_NUMERIC=sv_SE.UTF-8 sets the decimal mark to "," instead of ".". This causes crash with error in configuration.c when for example starting a reconstruction in HawkGUI. Can be fixed by setting LC_ALL=en_US-UTF-8 .

Some of the transformations during stitching don't work.
They should be disabled until they are fixed.

When using the Center Image option under the Support Update Method tab, the error of the real image spikes because the particle jumps outside of the support. This does not occur when Center Image is disabled.

On the binary packages, check if CUDA is installed and give a sensible error message.

It should be possible to measure absolute distances in the GUI.

Hello, I am trying to install Hawk on my mac and ubuntu workstation. In both cases, it was stopped the following error message:

CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
SPIMAGE_INCLUDE_DIR

How can I overcome this error?

Best regards,

Maximizing contrast seem to make everything dark.

It's not possible to select if we want to use the CPU of GPU through the graphical interface of the configuration file.