Closed e-larsson closed 2 years ago
*.project.compilation: Skipped index 0 image
Please make an issue out of this and place it in modernize SoM project and top priority.
Grayscale has slight differences in coordinates and decimals in values Orientation marks slightly different FixturePlateModel coordinates slightly different
Several detection methods are not deterministic so slight differences are expected, but if one plots the grayscales next to each other they ought to be extremely similar in shape and more or less lie on top of each other.
The original image is something like 4800x6000 pixels and the coordinates errors for orientation marks and fixture plate model should as a relative error be very small.
2022-01-28 08:21:55 -- ERROR Compile Effector Could not output analysis to file /somprojects/PayamMartin19Oct16Scanner2/PayamMartin19Oct16Scanner2_0000_30.2968.tiff
This is really weird error, I suppose it output the result of the compilation somewhere? Probably make an issue for this because it would be very bad if it attempts to overwrite images.
image_*_data.npy
The file with the last index is missing, due to missing index 0 in compilation probably The numbers are different by about factor 2
I agree that it's probably the missing image 0, so if you compare e.g. old index 3 with new index 2 are the numbers still that off?
phenotypes_filter.npy
Old one can't be opened
@skymandr this shouldn't be created anymore should it?
phenotypes_filter.npy
Old one can't be opened
@skymandr this shouldn't be created anymore should it?
The one I fixed and deprecated was phenotype_params.npy
. Don't think this one came up as problematic in QC. But yeah, looks like it might need conversion.
phenotypes_filter.npy
Old one can't be opened
@skymandr this shouldn't be created anymore should it?
The one I fixed and deprecated was
phenotype_params.npy
. Don't think this one came up as problematic in QC. But yeah, looks like it might need conversion.
I can at least load it manually:
In [3]: np.load('../Projects/PM2/PayamMartin19Oct16Scanner2/analysis/phenotypes_filter.npy', allow_pickle=True)
Out[3]:
array([{<Phenotypes.InitialValue: 12>: array([[0, 0, 0, ..., 0, 0, 0],
...
Part of #141
Part of the task was to validate that the results are the same as in the old project, and they are not. They seem to be different right from the initial project compilation step so not really sure it is due to the feature extraction.
Here is a summary of what I found
2 - Compile Project
With local fixture
Produces
*.project.compilation
*.project.compilation.instructions
Differences
*.project.compilation
Errors
2022-01-28 08:21:55 -- ERROR **Compile Effector** Could not output analysis to file /somprojects/PayamMartin19Oct16Scanner2/PayamMartin19Oct16Scanner2_0000_30.2968.tiff
3 - Analysis
With dynamic positioning
Produces
grid_plate___*.npy
grid_size___*.npy
time_data.npy
image_*_data.npy
Differences
grid_plate___*.npy
Same shape but slightly different values by single digits
image_*_data.npy
time_data.npy
4 - Feature extraction
Run with overwriting QC
Produces
curves_raw.npy
curves_smooth.npy
normalized_phenotypes.npy
phenotype_params.json
phenotypes.Absolute.plate_*.csv
phenotypes.extraction.instructions
phenotypes_filter.npy
phenotypes_meta_vector_raw.npy
phenotypes_raw.npy
phenotypes_reference_offsets.npy
phenotype_vectors_raw.npy
phenotype_times.npy
Differences
curves_raw.npy
andcurves_smooth.npy
phenotypes.Absolute.plate_*.csv
phenotypes_filter.npy
phenotypes_raw.npy
phenotype_vectors_raw.npy
phenotype_times.npy