SWC-Advanced-Microscopy / measurePSF

Measure PSF FWHM along different axes
GNU Lesser General Public License v3.0
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Labels missing or need modifying in measurePSF #52

Closed raacampbell closed 4 years ago

raacampbell commented 4 years ago
raacampbell commented 4 years ago

My screenshot in the GUI looks like this: Screen Shot 2020-04-03 at 17 16 35

There are FWHM labels as expected.

raacampbell commented 4 years ago

Indeed with Bruno's noisier bead there are no labels. Screen Shot 2020-04-06 at 21 40 31

raacampbell commented 4 years ago

Aha:

>> Copying PSF fit to base work space as variable "PSFstats"
>> PSFstats

PSFstats = 

  struct with fields:

          fitStats: [1x1 struct]
          PSFstack: [51x51x80 double]
    micsPerPixelXY: NaN   <---
     micsPerPixelZ: NaN   <---
    figureSnapshot: [900x900x3 uint8]

It's been re-saved in ImageJ and the pixel sizes are missing:

>> tmp=imfinfo('~/Downloads/PSF_2020-53-28_15-02-54_00001.tif')
>> tmp(1).ImageDescription

ans =

    'ImageJ=1.52i
     images=80
     slices=80
     unit=micron
     cf=0
     c0=-32768.0
     c1=1.0
     vunit=Gray Value
     loop=false
     min=33295.0
     max=33324.0
     '
raacampbell commented 4 years ago

Then it reports nothing because of this in the constructor:

if exist('micsPerPixelZ','var') && isnumeric(micsPerPixelZ) && isscalar(micsPerPixelZ)
      obj.micsPerPixelZ = micsPerPixelZ;
      obj.reportFWHMz=true; % THIS STOPS IT REPORTING
end

This is fine, but the user doesn't know about it. Need to change the plot labelling so it's clear what's happened.

raacampbell commented 4 years ago

7d5465d08d6461e9590855cf2efe67dc2d3ac886 reports to screen if no mics/pix provided for Z. Also prints to the command line whether this information is missing in XY and in Z. Screen Shot 2020-04-07 at 08 34 08

raacampbell commented 4 years ago

Report on figure for XY also: d85d78808631dbbdcd9f8ba12d3e66974e650c56