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DECODE_training_estimates #8

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kaarjel opened this issue Aug 9, 2022 · 11 comments
Open

DECODE_training_estimates #8

kaarjel opened this issue Aug 9, 2022 · 11 comments

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@kaarjel
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kaarjel commented Aug 9, 2022

Dear Jonas,

I am trying to generate the .yaml file for getting the DECODE training parameters but I seem to be getting an error message here. The screenshot of the issue is below. I localised some raw frames and also loaded the 3D cal into the 'Fitter' tab. However after rendering the image, when I click on 'Use parameters from current SML file', I get the UI Control Callback error. This SMAP is the MATLAB version.

Could you please advise where I am going wrong?

Best wishes,
Kaarjel

image
@Haydnspass
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Dear Kaarjel,

which branch are you on?

@kaarjel
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kaarjel commented Aug 9, 2022

Dear Lucas,

I'm not sure how to get that info...I downloaded the .zip folder and installed SMAP following the instructions in the Github page. Is this not the right installation?

image

Best wishes,
Kaarjel

@Haydnspass
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That sounds good. Could you send us your fit (the sml file) and if possible the frame? Then we can try to reproduce the error.

@kaarjel
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kaarjel commented Aug 9, 2022

That's great, thanks for checking. Here's a folder containing the sml file and one frame.

FittingData_SMAP.zip

@Haydnspass
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Dear Kaarjel,

We figure your error is that the decode environment is not correctly found. Have you installed decode according to the installation instructions? https://decode.readthedocs.io/en/release-0.10/installation.html
After that, you should check the location of the decode environment in the SMAP settings.

image

@kaarjel
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kaarjel commented Aug 15, 2022

Dear Lucas,

Thanks for following up on this. I installed decode several months ago according to the instructions but didn't have time to follow up on it. Now I changed the environment path in SMAP but the error still persists (please see below). Did the files I sent you work for you?

image

@Rieslab
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Rieslab commented Aug 15, 2022 via email

@kaarjel
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kaarjel commented Aug 16, 2022

Dear Jonas,
Thanks for picking up on this. Please find the content below. I think I'm on the main branch... In terms of the .yaml file I think it's in the folder; I've included a screenshot below with the highlighted file so you can double-check.
Best wishes,
Kaarjel

>> SMAP
main directory: D:\SMAP\SMAP-master\SMAP
settings directory: settings
plugin help directory: Documentation\help
bioformats package not found. Please select path to bioformats_package.jar in the Preferences.
you can download the Matlab toolbox for bioformats at  https://www.openmicroscopy.org/bio-formats/downloads/
git: On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:

Error using javaObjectEDT
No class org.micromanager.acquisition.TaggedImageStorageMultipageTiff can be located on the Java class path

Error in imageloaderMM/openi (line 24)
            obj.reader = javaObjectEDT('org.micromanager.acquisition.TaggedImageStorageMultipageTiff',fileparts(file), false, [], false, false, true);

Error in interfaces.imageloaderSMAP/open (line 227)
                    obj.openi(file)

Error in interfaces.imageloaderSMAP (line 37)
                obj.open(varargin{1});

Error in imageloaderMM (line 14)
            obj@interfaces.imageloaderSMAP(varargin{:});

Error in imageloaderAll (line 42)
        [io]=imloader(varargin{:});

Error in WorkflowModules.Loaders.TifLoader/addFile (line 198)
            obj.imloader=loader(file,obj.getPar('loc_fileinfo'),obj.P);

Error in WorkflowModules.Loaders.TifLoader>loadtif_callback (line 302)
    obj.addFile(f);
simple tiff loader loader
no description found
could not determine number of images. Directly evaluate file, might take time.
Camera not recognized. Use default
CUDA driver version: 11020
CUDA driver version: 8000
CUDA devices detected: 1
Using GPU GeForce RTX 2060 SUPER
subregion size: 7 fittype: 1
Number of fits: 1 no padding
Memory required: 0MB Memory available: 8192MB
threadx: 64,blockx: 1
Memory copies to GPU 0.176592 seconds
Actual fitting time 0.001192 Actual fits per second 838.996560
Memory copies from GPU 0.000182 seconds
Clean up from GPU 0.000146 seconds
using: GPUmleFit_LM_NoRestrict
564 localizations in 1.3129 seconds.
files
history
saved as version -v7.3
close imloader
fitting done
Unrecognized function or variable 'readlines'.

Error in ReadYamlSimple (line 2)
ln=readlines(file);

Error in Analyze.calibrate.DECODE_training_estimates/initGui (line 123)
            obj.yamlpar=ReadYamlSimple(yamldefault);

Error in interfaces.GuiModuleInterface/makeGui (line 700)
            obj.initGui; %exchanged

Error in interfaces.DialogProcessor/makeGui (line 34)
            anyoptional=makeGui@interfaces.GuiModuleInterface(obj,guidef);

Error in makePluginMenu>makeplugin (line 147)
    module.makeGui;
 
Error while evaluating Menu Callback.

Warning: Converting X to matrix of double. 
> In curvefit.attention/Warning/throw (line 30)
  In fit>iFit (line 150)
  In fit (line 116)
  In meanexp (line 30)
  In make_statistics2>meanexphere (line 519)
  In make_statistics2 (line 158)
  In Analyze.calibrate.DECODE_training_estimates>usecurrent_callback (line 338) 
Warning: Ignoring extra legend entries. 
> In legend>process_inputs (line 602)
  In legend>make_legend (line 334)
  In legend (line 278)
  In make_statistics2 (line 162)
  In Analyze.calibrate.DECODE_training_estimates>usecurrent_callback (line 338) 
Warning: Converting X to matrix of double. 
> In curvefit.attention/Warning/throw (line 30)
  In fit>iFit (line 150)
  In fit (line 116)
  In meanexp (line 30)
  In make_statistics2>meanexphere (line 519)
  In make_statistics2 (line 229)
  In Analyze.calibrate.DECODE_training_estimates>usecurrent_callback (line 338) 
Warning: Equation is badly conditioned. Remove repeated data points or try centering and scaling. 
> In curvefit.attention/Warning/throw (line 30)
  In fit>iLinearFit (line 680)
  In fit>iFit (line 391)
  In fit (line 116)
  In make_statistics2 (line 294)
  In Analyze.calibrate.DECODE_training_estimates>usecurrent_callback (line 338) 
read noise set to 74.4 e- for EM gain
emitters in 40x40 per frame: Inf
Reference to non-existent field 'InOut'.

Error in Analyze.calibrate.DECODE_training_estimates>usecurrent_callback (line 381)
    if isempty(js.InOut.calibration_file)
 
Error while evaluating UIControl Callback.

>>

image

@Rieslab
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Rieslab commented Oct 11, 2022 via email

@phoess
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phoess commented Oct 11, 2022

We had a similar problem in the lab recently, this function was introduced in the MATLAB version 2022a. Yu-Le wrote a fix for this (implementing the function separately) on the develop branch:
9265797

Philipp

@kaarjel
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kaarjel commented Oct 13, 2022

Dear Jonas,
I am using the 2020a version.

Dear Philipp,
Thank you for directing me to this. Mine is an older MATLAB version but I will give it a try to see if it works for me too.

Thank you both,
Kaarjel

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4 participants
@phoess @Rieslab @Haydnspass @kaarjel