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Makes usage of ROIs more transparent.

• add image id property
• add roi id property

i.e. compile bhfield for macOS

https://github.com/RI-imaging/DryMass/runs/2252081619?check_suite_focus=true

This happens with particularly large objects

Required to make labeling of excluded ROIs (see #5) consistent with selection of background images (counting starts at 1).

major and minor radius
volume computed by a rotational symmetry

I got the following error when applying dm_analysis_stretch

the am_analysis_sphere performed without error, but seems that there were issues too:

For some reason, ImageJ cannot open compressed TIFF files generated with tifffile.py when the data stored consists of a two-channel floating point image.

workaround: disable compression for now

dm_analyze_stretch.exe (edge projection) does not work recursively like dm_analyze_sphere.exe (edge projection or image rytov-sc) does.

No sure why, but I do not get negative values, for the phase line plot, at the edge of the drop. Any idea?

When starting overnight long time analysis (e.g. image rytov-sc) the PC pauses the analysis.
I changed some of the power saving settings, but that seems to help only partially.
Any recommendation?

This information might be important when comparing different setups. If e.g. PBS is used as a buffer solution, the RI of water might play an important role. Maybe this should go into the docs or a feature could be added that performs a correction according to this table:

ri_water.txt

*statistics.txt files do not contain the time and dry_mass information. Is there any specific reason to not have it? If not, for further analysis, would be good to have it in these files too.

• simple bead HL60 cell measurements, preferably from previous paper
• upload to "QPI-data" repository in RI-imaging
• optional intensity background correction with new "guck" file format in qpformat?
• statistics plot of results, reproducing figure in paper

• sample where ROI image contains artefacts
• compare and explain background correction methods

'Case when a directory containing measurements without any subdirectory is given'

when applying ' dm_analyze_sphere.exe -r 'g:\00_test'' a new directory is created, dir1_dm, at the main location:

Also a new directory is created at main_location\dir1\dir_dm:

• I guess the correct operation should be:

This is useful when one has several measurements with different parameters in one section (e.g. meta) and only wants to globally modify parts of another section (e.g. sphere) when running with the --profile and --recursive flags.

TODO:

• update implementation in dialog.py (line 115)
• test functions

Originally posted by @gcojoc in https://github.com/RI-imaging/DryMass/issue_comments#issuecomment-430917055

Compare several approaches for three images:

• perfect image
• image containing background ramp
• image containing other phase objects

DryMass identifies image with a series identifier and an index. It would be nice to have the file name there as well, because it usually contains important information about the measurement.

To avoid long identifiers, the file name could be stripped of the common prefix/suffix within the series.

Required for tomography analysis.

Currently, I'm acquiring phase data of drops for20s/~70frames per drop. It is kind of pain to apply for each time manually "dm_analyze_sphere.exe "main_folder\folder_name\folder_name.zip" ".

• assert backwards compatibility (value in [None, "none", ..., "nan"])
• update parsers
• update dialog functionalities
• update background handling methods

related with #19

• when created the 'main_location\dirXY\dirXY.zip_dm' directory, a drymass.cfg file should be placed inside. The drymass.cfg file should contain the same RI of the medium, pixel size, wavelength, sample size +- deviation, eccentricity +- deviation and name of background correction image (SID PHA bg.tif) for all directories in the main folder. An option can be that a drymass.cfg file is manually placed by the user at the 'main_location' or the software ask in the beginning for these imput parameters. #19

This is more user convenient and pythonic.

There are cases of stack/serie of imagines in which not all the frames have an object to be analyzed. When performing stretch mode analysis, the software will stop analyzing that stack (and any other recurent stack) and not save the images analyzed, although the computed data is printed in the xx_statistics file.

• this file will be excluded from the analysis (should be done manually, see #5)
• all images will be background corrected with this file
• use for intensity and phase separately

When performing recursive analysis on stretch mode, software stops at the instance it founds an error.
Wouldn't be better to report the error and pass to the next instance without stopping?

• Barer, Refractomety of Living Cells I, page 416 (valid until limit of solubility of bovine plasma albumin)