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License: MIT License
It has been suggested that we will need a workflow manager to bind together the different components. Let's use this issue to list and discuss the different options.
More suggestions?
Scientists and microscope facility engineers need to be able to easily change metrology workflows and manage pipelines. Integrating microscope-metrics with a workflow manager can offer the possibillity to modify pipelines in a modular way. Using such a framework also permits adding analysis and ML features.
Possible solutions:
Things to keep in mind:
There is a place for a comment as an output but there is no way to give a comment when running an analysis
Currently the input analysis parameters are not reflected in the log. This should be the case.
We should probably run a number of predefined tasks before running the analysis:
Here are the main steps of the Field Illumination algorithm.
1- Image is split into individual channel images.
2- (opt) Each channel is blurred (Gaussian blur, sigma 2.0) [mind this influences the next step as it may remove saturated noise pixels]
3- Saturation is measured
4- A fia (field illumination array) class is created for each channel. This arrays stores coordinates
5- ImageStatistics are computed for each channel.
11- Profile images are generated by drawing an intensity/coordinates plot along the remarkable lines.
FutureWarning: multichannel
is a deprecated argument name for gaussian
. It will be removed in version 1.0. Please use channel_axis
instead.
This is shooting a warning
Analysis date and time is not provided as output.
We need some images to test the analysis of field illumination
It has been discussed that we would need a Dashboard application to visualize the data. Let's use this issue to list and discuss the options. Links ar etowards the galleries of the different solutions.
More options?
The different analysis have to do a number of validations that are going to be generic to any analysis, such as if all the required parameters are in place.
We can generalize those within the run function and make this one call a private _run that is override in the analysis subclass
We would like a separate library for plotting the output (and input) data that is provided by microscope-metrics.
We could call it something like microscope-metrics-viz/plots/graphs/gallery.
Microscope-metrics does not currently raise error exceptions. At the moment the module solely logs activity. Implementing error handling also entails identifying possible errors and their meaning to users.
An example of a possible error in this project is a saturation error when the saturation present on an image does not permit deducting viable metrics.
It seems that isort conflicts with blacked in the way we format multiple imports. I'd rather have blacked so for the moment I deactivate isort
FutureWarning: The 'mad' method is deprecated and will be removed in a future version. To compute the same result, you may do (df - df.mean()).abs().mean()
.
We need to find a proper way to serialise the output measurements;
Must be compatible with numpy arrays.
The color of ROIS fill and strokes is implemented as a tuple. Pydantic's Color type would be way more flexible.
FutureWarning: indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.
indices true will make the function return the mask for the maxima. Unfortunately we do not use the default bahaviour.
It might be easier to work with xarrays in stead of numpy arrays.
We need to provide type hinting for, at least, all the exposed functions.
We will have to go through the code and verify it.
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