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Coloc 2

1 byte added, 09:31, 6 August 2015
To Do List: reorder list to put fixed stuff at bottom. - would be nice to have a "bugs fixed - news" section on the page... so wont delete it yet.... maybe there is a way to link to the githum issue tracker closed issues?
# Bug tracker issue no.17 Add Tests and implementation for %Colocalization by intensity and pixels(or voxels) wrt each channel, as per the depreciated Colocalization Threshold plugin - force use of a ROI or mask, as only then do these measures make sense. Add docs for this.
# Fixed in chalkie666 github repo:
## Numerical results and image stats are currently spewed into the IJ.log window. This is done separately from the way results are put into the simple results display window or the PDF output. So there three differently formatted results outputs with different stuff in them. Different ResultsHandler implementations like PDF or Simple can and do show a different selection of results. This is over complicated, so it should be made into one thing, that outputs the same numerical results and stats values, in the same order in all ResultsHander implementations ( GUI display and PDF output, and also the IJ.log. Can reuse the ValueResults class for all three by doing the same thing in each ".
### Make IJ.log writing only happen once and only in SimpleWindowDisplay - the default ResultHandler that's always used.
### get the Coloc job name from the DataContainer image names, and also add the mark/ROI OD to the job name in case there are multiple ROIs.
# Missing Feature?: implement flags in GUI to turn on and off desired output values??? Or does this break the idea of having a standardized output? Perhaps instead just make sure the IJ.log output is easily parse-able by humans and machines.
# Bug: Large images don't fit in results display gui, and there are no scroll bars.
# Enable use multi-channel images as well as the current 2 images (one channel each) plus 1 mask image selection. Need to choose which images in the multi-channel images if there are more than 2.... or even which 2 channels and which mask images, if the multi-channel image contains 3 or more channels. This avoids the user having to run split channels. Ease of use.
# Change channel naming convention in output using imagename1 and imagename2 to use imagename1(Ch1) and imagename2(Ch2), so its clear which is ch1 and ch2
# Fixed in fiji master github repo:
## Running as imageJ macro command fails because of the parameter: show_"save_pdf"_dialog. Probably the "" are messing up the run(Coloc_2, "params"); text string parameters. So need to escape out or get rid of the "" around save_pdf... why are they there? Just to look nice apparently?
# Running as macro need a method / GUI parameter to make the PDF file output saved without user interaction.
# Running as macro command in a loop, need to use macro commands to save the IJ.log window results, then clear the log window before the next set of results are sent there. Add words to documentation to explain that.
# Fixed in chalkie666 fiji master github repo trivial bug:
## if 2D histogram regression finds a y intercept that is below zero it gives the too high warning "Warning! y-intercept high - The absolute y-intercept of the auto threshold regression line is high. Maybe you should use a ROI, maybe do a background subtraction in both channels" So should change warning text to too high or too low depending on if its positive or negative.
# Fixed in fiji master github repo:
## Numerical results and image stats are currently spewed into the IJ.log window. This is done separately from the way results are put into the simple results display window or the PDF output. So there three differently formatted results outputs with different stuff in them. Different ResultsHandler implementations like PDF or Simple can and do show a different selection of results. This is over complicated, so it should be made into one thing, that outputs the same numerical results and stats values, in the same order in all ResultsHander implementations ( GUI display and PDF output, and also the IJ.log. Can reuse the ValueResults class for all three by doing the same thing in each ".
### Make IJ.log writing only happen once and only in SimpleWindowDisplay - the default ResultHandler that's always used.
### get the Coloc job name from the DataContainer image names, and also add the mark/ROI OD to the job name in case there are multiple ROIs.
# Fixed in fiji master github repo:
## Running as imageJ macro command fails because of the parameter: show_"save_pdf"_dialog. Probably the "" are messing up the run(Coloc_2, "params"); text string parameters. So need to escape out or get rid of the "" around save_pdf... why are they there? Just to look nice apparently?
== DONE ==