Automatically save reslices and max-projections

[ffvoigt]

This is intended both to streamline quality control checks and to debug acquisitions.

Users should be able to select one of the following options for each row in the Acquisition Manager:

• save xy max projection of the stack (most important)
• save full xz / yz reslices of the stack (xz has priority)
• save maximum projections of full and partial reslices (e.g. select to split the resliced volume in 1 to 10 subvolumes and do a partial reslice there)

This way, for a single stack, multiple datasets can be created on the fly:

This will require touching the following parts of the code:

• in the camera thread (mesoSPIM_Camera.py), the computations should be executed
• add a corresponding row to acquisitions.py (e.g. a dictionary that allows specifying which online-processing steps should be taken and with which parameters)
• add a delegate in delegates.py to have a button that opens a GUI (e.g. a wizard) to specify which processing steps should be executed

Here is some code from my experiments with this in the camera thread:

In prepare_stack():

self.xz_stack = np.memmap(self.path[:-4]+'xz.raw', mode = "write", dtype = np.uint16, shape = 2048 * self.max_frame * 2048)
self.yz_stack = np.memmap(self.path[:-4]+'yz.raw', mode = "write", dtype = np.uint16, shape = 2048 * self.max_frame * 2048)

In add_images_to_stack():

''' Write YZ (coronal) image '''
for j in range(2048):
    line =  data[j*2048:(j+1)*2048]
     self.yz_stack[2048*j*self.max_frame+2048*self.cur_frame:2048*j*self.max_frame+2048*self.cur_frame+2048] = line

In end_stack(), one should make sure to delete the self.yz_stack object as it might need a lot of memory.

[alecrimi]

using the code as describer in "add_images_to_series()" the resliced volume seems to have the lines ordered sequencially rather than rotated. See picture below with original slice (left) and resliced (right)

[ffvoigt]

I think you have to open the stack differently in Fiji: Import as raw, then set the X & Y according to the stack parameters (e.g. 2048 pixel width for X times number of z-steps for Y). Number of images should be 2048. For a YZ reslice, you have to change the import values accordingly.

[alecrimi]

I have now linked the reslicing and maxproj to delegates of the AcquisitionManagerWindows. By default all values are "no", namely unless the user changes the this from the gui no max projection or reslicing is computed. The are some IFs statement in mesoSPIM_camera.py that check whether the value is "no" or "yes" and in case compute and save the reslicing or the max projection. The Wizard still needs to be implemented

[ffvoigt]

Can you put this in a branch somewhere where I can see it?