Image dimension stacking #495
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hamshkhawar
requested review from
Nicholas-Schaub and
NHotaling
as code owners
Apply Sweep Rules to your PR?
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| 1. multi-channel `groupBy=c`\ | ||
| For example `filePattern=x01_y01_p01_c{c:d+}.ome.tif` | ||
| 2. multi-zplanes `groupBy=z`\ | ||
| For example `filePattern=tubhiswt_C1-z{z:d+}.ome.tif` | ||
| 3. multi-timepoints `groupBy=t`\ | ||
| For example `filePattern=img00001_t{t:d+}_ch0.ome.tif` |
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Add examples for when we have multiple variables and dimensions that are being stacked at once.
| [[tool.poetry.source]] | ||
| name = "test" | ||
| url = "https://test.pypi.org/simple/" | ||
| default = false | ||
| secondary = true |
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This section should be removed
| raise ValueError(msg) | ||
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| if preview: | ||
| generate_preview(out_dir=out_dir, file_pattern=file_pattern) |
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Plugin should return after generating the preview.
| if group_by == "c": | ||
| bw.C = dim_size | ||
| if group_by == "t": | ||
| bw.T = dim_size | ||
| if group_by == "z": | ||
| bw.Z = dim_size | ||
| bw.ps_z = z_distance(input_files[0]) |
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The check should be for whether c, z or t are variables in the input filepattern, and not whether they are in (or equal to) the group_by input. Stacking should be done on all axes together.
| input_files = [] | ||
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| fps = fp.FilePattern(inp_dir, file_pattern) | ||
| out_name = fps.output_name() |
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The output should be in a per-group basis.
| bw=bw, | ||
| ) | ||
| threads.append(thread) | ||
| pm.join_threads() |
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This function will block and will not return until all jobs are finished. The following tqdm progress bar is useless.
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See my comments from the PR with CZI Extraction plugin for this file.
hamshkhawar
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* new plugin * refactored code and added pytests * adding plugin json and correcting documentation * fixed documentation * fixed documentation * fixed documentation * fixed documentation * fixed documentation * updating docker base container * added multiple pattern support * added docstring * fix plugin name and test fixture * test cli * fixing multipattern test * fix slow test * fix slow test
This plugin will allows stacking of multidimensions (channel, timepoints, z-planes) and will be replacing functionalities of two existing plugin